Suddenly one of my workers landed in one of charlemanges cities and he lost 2 cities when i took 1...

wrong forum - this should go into the BtS bug reports ;)
Anyway: it is a known bug caused by teleporting workers - install Bhruic's Unofficial Patch for 3.13 (stickied in main BtS forum) and all is good :) :goodjob:

I just had the exact same bug with the HOF mod for BtS 3.13...

I have seen that and I am surprised - that was one of the first bugs fixed by Bhruic and should be implemented there - apparently they need to fix the HOF-Mod :)