If you've registered more episodes on the target site no update to it will be made.
If you've rated a show on trakt it will overwrite the existing one.
The season rating will be used for each individual entry if present and otherwise fall back to the show level. This might lead to some unexpected scores but you'll be shown all updates and you can easily adjust them with another rerun.
**Movies entries which are actually multiple OVA episodes.**
→ TMDb follows the first released format, and does not allow "duplicated" content between the Movie and TV Show sections. People tend to readded this stuff despite being invalid. It can sometimes also take them a while to correct things (eg. Battle Angel Alita which was recut as a Movie for the US but was actually a two episode OVA in Japan).
**Episodes in the "Special" Seasons** (which are mostly indivudual OVAs or specials)
→ Frankly this would require a lot of additional effort for very little gain and the Episodes within tend to be moved around or be removed due to not being the proper specials anyways.