When I checkout different branches, I sometimes notice that files in the repo are not available to Vim plugins that search based on the ctags index.
I don't have a definitive test that's shown the files are missing due to versioning, but I usually notice that the missing files are those that were recently added.
I occasionally notice other missing lookups, e.g. with function names or other symbols, and assume it's the same matter. I'll quickly provide any details if someone has ideas.