I’ve tried a few ways to test this out on a couple of different sites I’m on, and I can’t find a way that doesn’t confuse me. 
No clear answer for you, but this is what I did:
- Set a category to tracking
- Wait for all the background jobs to kick in
- Have lots of blue unread and new markers on old topics
- Check for individual topic tracking status. Lots were Tracking, some weren’t
- Dismiss all from New and Unread
- Got some more blue markers (maybe the background jobs still ticking away)
- Dismissed those too
- Eventually got only new stuff showing. None missing.
I think that me dismissing them (though not clearing tracking) may then spoil that forum for another test with that category.
No idea if that is helpful, but didn’t want you to think no one was listening.