I installed the last pre 1.0 version of aTV flash (black) a while ago. Now I see that 1.0 and 1.1 has been released.
If I install 1.1 now, will I lose my “watched/unwatched” data on Apple TV, as well as other settings there might be (either in aTV Flash or on AppleTV itself)?
Settings, metadata, watched history, etc… are only affected in you restore or rejailbreak the AppleTV.
Updating the version will not affect these, but if you want to be safe you can always do a backup through the Maintenance --> Settings menu. Doing this will take a snapshot of the current settings on the AppleTV which you can easily roll back to if needed.