You can remove the directory and its files from your local repository using git rm
and committing the change.
When you next want to rebase against the upstream branch, you will have no problems if the upstream has not made any changes to those files you have removed. You changes can be applied without any interactive attention.
However, if the upstream has modified any of those files, git rebase
will show a conflict and ask you what to do. When this happens, you can resolve the conflict by removing the file(s) in conflict and continuing the rebase. When you complete the rebase, those files will still be removed in your local repository.