What is git thinking?

I don't understand what git is thinking sometimes. In SourceTree, I pulled the latest code from the repository with rebase selected, it told me it couldn't apply a patch, and to resolve the issue manual and then continue the rebase from a git shell.

So I proceeded to do that. One thing I noticed was that git deleted one of my files!!! <-- What on Earth is git thinking? Why would it ever think of deleting a file in response to rebase issues? No one on the team deleted it. There was absolute nothing wrong with the file, and when I undid the deletion, and finished the rebase, the file worked just fine.

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Its difficult to comment without understanding more of the context, is it possible the file was deleted by one commit but restored by another and hence if appeared to have dissappeared because the rebase paused part way through?

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