Rebase doesn’t happen in the background. “rebase in progress” means that you started a rebase, and the rebase got interrupted because of conflict. You have to resume the rebase
(git rebase --continue) or abort it (git rebase --abort).
As the error message from git rebase --continue suggests, you asked git to apply a patch that results in an empty patch. Most likely, this means the patch was already applied and you want to drop it using git rebase --skip.