Restarting Sublime usually results in all files in the project being reindexex (indexing progress starts from 0). It’s a big project (Chromium repo) so it takes quite a lot of time and CPU to finish so I’d rather avoid it.
Sublime 3 3052, Mac OSX. I don’t have this problem on Windows.
I’ve even deleted ~/Library/Application Support/Sublime Text 3/Index thinking that some files might be in a bad state but that didn’t help. Indexing still restarts from scratch after restart.