I think you have some other problem other than the one you have described. My Find Weakness list is still 79 items in length and clearly visible in the savedata.txt file from the KBScanner. Search for "assassin_exp" in that file. I've been in and out of the Wizard's Tower multiple times and my assassins are doing just fine and never have been reset.
I'm currently stuck on the tower level that duplicates your troops for the wizard team and trounces me badly.
