diff --git a/src/Xamarin.Android.Build.Tasks/Tasks/BuildApk.cs b/src/Xamarin.Android.Build.Tasks/Tasks/BuildApk.cs
index d1075ef0376..1b75f8fe840 100644
--- a/src/Xamarin.Android.Build.Tasks/Tasks/BuildApk.cs
+++ b/src/Xamarin.Android.Build.Tasks/Tasks/BuildApk.cs
@@ -122,46 +122,23 @@ void ExecuteWithAbi (string [] supportedAbis, string apkInputPath, string apkOut
 			}
 
 			ArchiveFileList files = new ArchiveFileList ();
-			bool refresh = true;
-			if (apkInputPath != null && File.Exists (apkInputPath) && !File.Exists (apkOutputPath)) {
-				Log.LogDebugMessage ($"Copying {apkInputPath} to {apkInputPath}");
-				File.Copy (apkInputPath, apkOutputPath, overwrite: true);
-				refresh = false;
-			}
+
 			using (var notice = Assembly.GetExecutingAssembly ().GetManifestResourceStream ("NOTICE.txt"))
 			using (var apk = new ZipArchiveEx (apkOutputPath, File.Exists (apkOutputPath) ? FileMode.Open : FileMode.Create )) {
-				if (refresh) {
-					for (long i = 0; i < apk.Archive.EntryCount; i++) {
-						ZipEntry e = apk.Archive.ReadEntry ((ulong) i);
-						Log.LogDebugMessage ($"Registering item {e.FullName}");
-						existingEntries.Add (e.FullName);
-					}
+				bool apkInputPathExists = apkInputPath != null && File.Exists (apkInputPath);
+
+				DateTime lastWriteOutput = DateTime.MinValue;
+				DateTime lastWriteInput = DateTime.MinValue;
+				if (apkInputPathExists) {
+					lastWriteOutput = File.Exists (apkOutputPath) ? File.GetLastWriteTimeUtc (apkOutputPath) : DateTime.MinValue;
+					lastWriteInput = File.GetLastWriteTimeUtc (apkInputPath);
 				}
-				if (apkInputPath != null && File.Exists (apkInputPath) && refresh) {
-					var lastWriteOutput = File.Exists (apkOutputPath) ? File.GetLastWriteTimeUtc (apkOutputPath) : DateTime.MinValue;
-					var lastWriteInput = File.GetLastWriteTimeUtc (apkInputPath);
-					using (var packaged = new ZipArchiveEx (apkInputPath, FileMode.Open)) {
-						foreach (var entry in packaged.Archive) {
-							Log.LogDebugMessage ($"Deregistering item {entry.FullName}");
-							existingEntries.Remove (entry.FullName);
-							if (lastWriteInput <= lastWriteOutput)
-								continue;
-							if (apk.Archive.ContainsEntry (entry.FullName)) {
-								ZipEntry e = apk.Archive.ReadEntry (entry.FullName);
-								// check the CRC values as the ModifiedDate is always 01/01/1980 in the aapt generated file.
-								if (entry.CRC == e.CRC) {
-									Log.LogDebugMessage ($"Skipping {entry.FullName} from {apkInputPath} as its up to date.");
-									continue;
-								}
-							}
-							var ms = new MemoryStream ();
-							entry.Extract (ms);
-							Log.LogDebugMessage ($"Refreshing {entry.FullName} from {apkInputPath}");
-							apk.Archive.AddStream (ms, entry.FullName, compressionMethod: entry.CompressionMethod);
-						}
-					}
+
+				for (long i = 0; i < apk.Archive.EntryCount; i++) {
+					ZipEntry e = apk.Archive.ReadEntry ((ulong) i);
+					Log.LogDebugMessage ($"Registering item {e.FullName}");
+					existingEntries.Add (e.FullName);
 				}
-				apk.FixupWindowsPathSeparators ((a, b) => Log.LogDebugMessage ($"Fixing up malformed entry `{a}` -> `{b}`"));
 				string noticeName = RootPath + "NOTICE";
 				existingEntries.Remove (noticeName);
 				if (!apk.Archive.ContainsEntry (noticeName))
@@ -248,6 +225,16 @@ void ExecuteWithAbi (string [] supportedAbis, string apkInputPath, string apkOut
 						count = 0;
 					}
 				}
+
+				// For now, we keep track of deleted entry indices & skip them ourselves when iterating zip contents in FixupWindowsPathSeparators.
+				// For this to work, no one shoud call Flush on the zip before calling FixupWindowsPathSeparators, since Flush changes all the indices
+				// (and gets rid of the deleted stuff). Later when we move to a newer LibZipSharp, with the fix to skip deleted entries itself,
+				// we can remove this workaround. See FixupWindowsPathSeparators for more info.
+				HashSet<ulong> deletedEntries = new HashSet<ulong> ();
+				if (apkInputPathExists)
+					UpdateEntriesFromInputApk (apkInputPath, apk, lastWriteOutput, lastWriteInput, deletedEntries);
+				apk.FixupWindowsPathSeparators (deletedEntries, (a, b) => Log.LogDebugMessage ($"Fixing up malformed entry `{a}` -> `{b}`"));
+
 				// Clean up Removed files. 
 				foreach (var entry in existingEntries) {
 					Log.LogDebugMessage ($"Removing {entry} as it is not longer required.");
@@ -258,6 +245,49 @@ void ExecuteWithAbi (string [] supportedAbis, string apkInputPath, string apkOut
 			}
 		}
 
+		private void UpdateEntriesFromInputApk (string apkInputPath, ZipArchiveEx apk, DateTime lastWriteOutput, DateTime lastWriteInput, HashSet<ulong> deletedEntries)
+		{
+			using (var packaged = new ZipArchiveEx (apkInputPath, FileMode.Open)) {
+				foreach (var entry in packaged.Archive) {
+					Log.LogDebugMessage ($"Deregistering item {entry.FullName}");
+					existingEntries.Remove (entry.FullName);
+					if (lastWriteInput <= lastWriteOutput)
+						continue;
+
+					long entryIndexInOutput;
+					if (apk.Archive.ContainsEntry (entry.FullName, out entryIndexInOutput)) {
+						ZipEntry e = apk.Archive.ReadEntry (entry.FullName);
+						// check the CRC values as the ModifiedDate is always 01/01/1980 in the aapt generated file.
+						if (entry.CRC == e.CRC) {
+							Log.LogDebugMessage ($"Skipping {entry.FullName} from {apkInputPath} as its up to date.");
+							continue;
+						}
+					} else {
+						entryIndexInOutput = -1;
+					}
+
+					var ms = new MemoryStream ();
+					entry.Extract (ms);
+
+					if (entryIndexInOutput != -1) {
+						Log.LogDebugMessage ($"Refreshing {entry.FullName} from {apkInputPath}");
+
+						// Force the modified resource to move to the end of the file, by deleting it first so that AddStream adds it
+						// back with a new index. Keeping modified resources toward the end optimizes the delta install for the typical
+						// dev scenario where the user is editing a few resources but most of the APK contents (e.g. the native libs)
+						// don't change and we want to keep their byte offset in the APK fixed. Delta install need not update APK
+						// contents that don't change and don't move.
+						apk.Archive.DeleteEntry ((ulong) entryIndexInOutput);
+						deletedEntries.Add ((ulong) entryIndexInOutput);
+					} else {
+						Log.LogDebugMessage ($"Adding {entry.FullName} from {apkInputPath}");
+					}
+
+					apk.Archive.AddStream (ms, entry.FullName, compressionMethod: entry.CompressionMethod);
+				}
+			}
+		}
+
 		public override bool RunTask ()
 		{
 			Aot.TryGetSequencePointsMode (AndroidSequencePointsMode, out sequencePointsMode);
diff --git a/src/Xamarin.Android.Build.Tasks/Tests/Xamarin.Android.Build.Tests/IncrementalBuildTest.cs b/src/Xamarin.Android.Build.Tasks/Tests/Xamarin.Android.Build.Tests/IncrementalBuildTest.cs
index c1d6353aac5..a6dd14f62b5 100644
--- a/src/Xamarin.Android.Build.Tasks/Tests/Xamarin.Android.Build.Tests/IncrementalBuildTest.cs
+++ b/src/Xamarin.Android.Build.Tasks/Tests/Xamarin.Android.Build.Tests/IncrementalBuildTest.cs
@@ -8,6 +8,7 @@
 using System.Text;
 using Xamarin.Android.Tasks;
 using Xamarin.ProjectTools;
+using Xamarin.Tools.Zip;
 
 namespace Xamarin.Android.Build.Tests
 {
@@ -1088,23 +1089,119 @@ public void AndroidResourceChange ()
 			using (var builder = CreateApkBuilder ()) {
 				Assert.IsTrue (builder.Build (proj), "first build should succeed");
 
-				// AndroidResource change
-				proj.LayoutMain += $"{Environment.NewLine}<!--comment-->";
+				// Change the AndroidResource body; just adding a comment isn't enough to trigger an APK update
+				string orientationTag = "android:orientation=\"vertical\"";
+				proj.LayoutMain = proj.LayoutMain.Replace (orientationTag, $"{orientationTag}  android:paddingLeft=\"16dp\"");
 				proj.Touch ("Resources\\layout\\Main.axml");
 				Assert.IsTrue (builder.Build (proj), "second build should succeed");
 
-				var targets = new [] {
+				AssertNonResourceTargetsSkipped (builder);
+			}
+		}
+
+		void AssertNonResourceTargetsSkipped(ProjectBuilder builder)
+		{
+			var targets = new [] {
 					"_ResolveLibraryProjectImports",
 					"_GenerateJavaStubs",
 					"_CompileJava",
 					"_CompileToDalvik",
 				};
-				foreach (var target in targets) {
-					Assert.IsTrue (builder.Output.IsTargetSkipped (target), $"`{target}` should be skipped!");
+			foreach (var target in targets) {
+				Assert.IsTrue (builder.Output.IsTargetSkipped (target), $"`{target}` should be skipped!");
+			}
+		}
+
+		[Test]
+		public void AndroidChangedResourcesAtEnd ()
+		{
+			var path = Path.Combine (Root, "temp", TestName);
+
+			var proj = new XamarinAndroidApplicationProject ();
+			using (var builder = CreateApkBuilder ()) {
+				Assert.IsTrue (builder.Build (proj), "first build should succeed");
+
+				string signedApkPath = Path.Combine (path, proj.OutputPath, "UnnamedProject.UnnamedProject-Signed.apk");
+
+				// Initial resources should at the end of the zip
+				using (var zip = ZipArchive.Open (signedApkPath, FileMode.Open)) {
+					Assert.AreEqual (37, zip.EntryCount, "Zip entry count");
+					AssertZipEntryHasPosition (zip, "res/layout/main.xml", 32);
+					AssertZipEntryHasPosition (zip, "resources.arsc", 33);
+				}
+
+				AndroidItem.AndroidResource layout2Resource = AddLayout2 (proj);
+				Assert.IsTrue (builder.Build (proj), "second build should succeed");
+
+				// Added resources should go at the end of the zip
+				using (var zip = ZipArchive.Open (signedApkPath, FileMode.Open)) {
+					Assert.AreEqual (38, zip.EntryCount, "Zip entry count");
+					AssertZipEntryHasPosition (zip, "res/layout/main.xml", 32);
+					AssertZipEntryHasPosition (zip, "res/layout/layout2.xml", 33);
+					AssertZipEntryHasPosition (zip, "resources.arsc", 34);
+				}
+
+				string orientationTag = "android:orientation=\"vertical\"";
+				proj.LayoutMain = proj.LayoutMain.Replace (orientationTag, $"{orientationTag}  android:paddingLeft=\"16dp\"");
+				proj.Touch ("Resources\\layout\\Main.axml");
+				Assert.IsTrue (builder.Build (proj), "third build should succeed");
+				AssertNonResourceTargetsSkipped (builder);
+
+				// Updated resources should go at the end of the zip
+				using (var zip = ZipArchive.Open (signedApkPath, FileMode.Open)) {
+
+					Assert.AreEqual (38, zip.EntryCount, "Zip entry count");
+					AssertZipEntryHasPosition (zip, "res/layout/layout2.xml", 32);
+					AssertZipEntryHasPosition (zip, "resources.arsc", 33);
+					AssertZipEntryHasPosition (zip, "res/layout/main.xml", 34);
+				}
+
+				proj.AndroidResources.Remove (layout2Resource);
+				Assert.IsTrue (builder.Build (proj), "fourth build should succeed");
+
+				// Removed resources should go away
+				using (var zip = ZipArchive.Open (signedApkPath, FileMode.Open)) {
+					Assert.AreEqual (37, zip.EntryCount, "Zip entry count");
+					AssertZipEntryHasPosition (zip, "res/layout/main.xml", 32);
+					AssertZipEntryHasPosition (zip, "resources.arsc", 33);
 				}
 			}
 		}
 
+		AndroidItem.AndroidResource AddLayout2 (XamarinAndroidApplicationProject proj)
+		{
+			const string layout2 = @"<?xml version=""1.0"" encoding=""utf-8""?>
+<LinearLayout xmlns:android=""http://schemas.android.com/apk/res/android""
+	android:orientation=""vertical""
+	android:layout_width=""fill_parent""
+	android:layout_height=""fill_parent""
+	>
+<Button
+	android:id=""@+id/myButton2""
+	android:layout_width=""fill_parent"" 
+	android:layout_height=""wrap_content"" 
+	android:text=""@string/hello""
+	/>
+</LinearLayout>
+";
+
+			var androidResource = new AndroidItem.AndroidResource ("Resources\\layout\\Layout2.axml") { TextContent = () => layout2 };
+			proj.AndroidResources.Add (androidResource);
+
+			return androidResource;
+		}
+
+		void AssertZipEntryHasPosition (ZipArchive zipArchive, string name, int expectedPosition) {
+			foreach (ZipEntry entry in zipArchive) {
+				if (entry.FullName.Equals (name, StringComparison.Ordinal)) {
+					Assert.AreEqual (expectedPosition, entry.Index, $"Zip entry {name} should be at expected position");
+					return;
+				}
+			}
+
+			Assert.Fail ($"Zip entry ${name} not found");
+		}
+
 		[Test]
 		[NonParallelizable]
 		public void AndroidXMigrationBug ()
diff --git a/src/Xamarin.Android.Build.Tasks/Utilities/ZipArchiveEx.cs b/src/Xamarin.Android.Build.Tasks/Utilities/ZipArchiveEx.cs
index a1d55647cb5..8ca2c7c0e41 100644
--- a/src/Xamarin.Android.Build.Tasks/Utilities/ZipArchiveEx.cs
+++ b/src/Xamarin.Android.Build.Tasks/Utilities/ZipArchiveEx.cs
@@ -1,4 +1,5 @@
-using System;
+using System;
+using System.Collections.Generic;
 using System.IO;
 using System.Linq;
 using Xamarin.Tools.Zip;
@@ -113,10 +114,25 @@ public void AddDirectory (string folder, string folderInArchive, CompressionMeth
 		/// <summary>
 		/// HACK: aapt2 is creating zip entries on Windows such as `assets\subfolder/asset2.txt`
 		/// </summary>
-		public void FixupWindowsPathSeparators (Action<string, string> onRename)
+		public void FixupWindowsPathSeparators (HashSet<ulong> deletedEntries, Action<string, string> onRename)
 		{
 			bool modified = false;
-			foreach (var entry in zip) {
+
+			long entryCount = zip.EntryCount;
+			if (entryCount < 0)
+				return;
+
+			for (ulong i = 0; i < (ulong) entryCount; ++i) {
+				// If an entry index has been deleted then ReadEntry will throw a "Entry has been deleted" ZipException.
+				// So we skip deleted entries instead. Later, when we move to a newer LibZipSharp (>= 1.0.13) with this fix
+				// https://github.com/xamarin/LibZipSharp/pull/53 we can remove this workaround and go back to using
+				// a foreach enumerator to enumerate the contents of the zip. With the fix, deleted entries are
+				// skipped on the LibZipSharp side when enumerating. But we want to keep the LibZipSharp bump as
+				// a separate change, with the other changes that come with it, and not depenend on that here.
+				if (deletedEntries.Contains (i))
+					continue;
+
+				var entry = zip.ReadEntry (i);
 				if (entry.FullName.Contains ('\\')) {
 					var name = entry.FullName.Replace ('\\', '/');
 					onRename?.Invoke (entry.FullName, name);