Nonexistent changes appear rebasing but only with rebase.backend=apply

Hi All

I'm facing a strange anomaly during rebase. I'll try to explain what happens because unfortunately I cannot share more information since it's confidential and unfortunately an anonymized export does not reproduce the issue.

I have the following repository status:

   * commit 2 (BRANCH X)
   |
   |  * commit 4 (BRANCH Y) (HEAD)
   |  |
   |  * commit 3
   | /
   |/
   * commit 1
   |
   |
 (...)

What I'm trying to do is rebasing branch Y on branch X, with the command: git rebase X

The anomaly is that, among other expected conflicts, also two files (fileA, fileB) appear modified in both branches, but those two files have not been modified in any of the 4 commits you see in the graph above! The anomaly appears only with the config setting rebase.backend=apply, while not with rebase.backend=merge (*).

This might not be caused by rebase command itself, but rather by some previous operations which might have accidentally "broken" something and that the rebase simply makes them appear. You need to know that commit 4 is the result of several squash and reordering of multiple commits; is it possible that some of those operations have created some "leftovers" ?

I know this is difficult without seeing the actual repository, but could you just give me some advice or point me to the place where I can investigate ?

(*) When the anomaly first appeared, I was using git for windows, version < 2.26.0 (unfortunately I cannot recover the exact number); I decided to upgrade git to 2.31.1 and the anomaly disappeared. Investigating the release notes, I noticed that rebase.backend default value changed from apply to rebase from version 2.26.0. I also copied the repository on linux (with git 2.31.0), and the behavior is the same.

Thanks in advance for any help, Best Regards, Marco