All flightpaths I've discovered is now undiscovered in the list. When I clickl on Flightmaster in location, (for example Dragon Isles) all gets discovered again (only for the zome)!

I guess your flightpaths cache has been cleared.
If it can be restored after visiting the flightmaster and it still exists in the next login, this may not be an issue.

Sounds like your saved variables for ATT somehow got wiped or cleared. Flight Paths are the only thing in ATT where you are required to interact with a FP on each continent for ATT to scan the known nodes.