Remove “deleted?” Files

[devkoa]

What i did:
git-filter-repo --analyze
Prepared the path-deleted-files.txt
and after run: git-filter-repo --invert-paths --paths-from-file ./path-deleted.txt

Everything worked fine and the tool did his job, but for my surprise after i faced some issues.
There was java classes completely deleted,and i cannot even build it. I could go through and remove the classes that i would like to keep from the list, but im wondering, since these classes still existing, why are removed?

Is there any flag that i can use, so the tool will not remove files that existing in Head, but only the previous versions?