I suspect that you need to understand how exactly does rebase.
When you run
git rebase master
, git will do this:
- you will find the beginning of the current branch
git checkout master
- in the loop will apply a single commit from the current branch, to the extreme. If there is a conflict, the process will be, git will prompt you to resolve the conflict, and then allow you to continue.
It's good behavior during the rebase.
In your case, I suspect there is a conflict, so git does not reach the commits where there are the files you need. If the conflict is to resolve and do
git rebase --continue
, the process continues.
Itself rebase removal of any file does not imply only the use of commits.
And surely noticed that rebase published branches should not do.