Meh, it's an easy situation to get out of though. Especially with a typed language and decent IDE: right-click, "inline function"; check your git status to see what changed, go to those files and remove unused branches (which a decent IDE should hightlight and provide 2-keystroke fixes for). 2 minutes, done.

Grotesquely replicated code is a much more difficult situation to resolve.

I'm guessing the OP primarily uses untyped languages. I'd offer that that is the core of the problem, not the abstractions.