Update warning if ckpt directory is not empty

[rohitgr7]

What does this PR do?

Fixes #5173

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[rohitgr7]

no @Borda, this doesn't resolve #4911. That's a different issue.

[codecov]

Codecov Report

Merging #5209 (e6641db) into master (be3e870) will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff           @@
##           master   #5209   +/-   ##
======================================
  Coverage      93%     93%           
======================================
  Files         134     134           
  Lines        9933    9933           
======================================
  Hits         9247    9247           
  Misses        686     686