KotDB: Brainking assigns points based on the current state of the game when the timeout occurs. I think worst case scenario is not practical to calculate.
I'm pretty sure that the correct way to resign cube match game is to offer your resignation along with the number of points you are resigning. If you resign a single point to me but I think I can gammon you, then I reject your resignation and we keep playing. Brainking doesn't support this. If you resign you give up the number of points on the board.
This being the case, you should never resign a cube match game until you have borne off a least one checker, and then only after it is mathematically impossible for you to win.