Accidental root pull when updating

So after probably re-reading the update instructions a couple of times, I still seem to have managed to fail on the first step and pull changes as (presumably) root on my previous update.

First I chowned the .git directory back to pleroma:pleroma as instructed in the #pleroma channel and I was allowed to pull, but the pull failed to unlink and create a bunch of files, breaking the web front end. I then asked if it's okay to just chown the entire pleroma directory, and was given green light (later realizing this was actually a step in the install guide). The problem is now that even after performing get reset --hard to get rid of unnecessary changes (as instructed by #pleroma), I suspect the ownership issues are still keeping a ton of files red in my git status. I assume I need to simply force the pull somehow? It won't pull normally as it says I would be "overwriting files".

Thank you in advance.