When switching git branches, several open files may be “deleted” from the working directory (because they’re not in the other branch). Next time Sublime saves, it’ll rewrite those files, which causes git to complain about overwriting them when switching back to the original branch.
This must be a fairly common problem given the popularity of git and I’m wondering if there are standard answers. From searching around, I didn’t find an obvious setting or plugin—although search results are overwhelmed with people trying to recover deleted files so it’s hard to tell.