Answer by raphinesse for git rebase: "error: cannot stat 'file': Permission denied"

This error can also be caused by the fact that files are still "locked" because of prior git actions. It has to do with how the Windows filesystem layer works. I once read a nice explanation on this, but I can't remember where.

In that case however, since it is basically a race condition, all you have to do is continue your interrupted rebase process. Unfortunately this happens to me all the time, so I wrote this little dangerous helper to keep my rebases going:

#!/bin/shset -egit checkout .git clean -dfgit rebase --continue

If you want to be extra sure, you can use git rebase --edit-todo to check if the next commit to be applied is really the one that failed to be applied before. Use git clean -dn to make sure you do not delete any important files.