Option 1: Don't update with the latest Repo changes.
Option 2: Go through each or your files one by one, manually merging updates from the Repo to the corresponding files.
Option 3: Start with clean copy of latest Repo, then manually merge your OWLTR and FS ATS changes into that. (This might be the best option if you commented the changes you made as you did them.)
Beyond those 3 options, there is not much else other than placing the shotgun up to the monitor and pulling the trigger.
But seriously, if you also have specific error messages, you are welcome to post those and see if they can be fixed one at a time.
Just please don't blindly merge changes from the Repo without saving your code, then post a million error messages here. Merging will not work well that way.