Steam support and 1C need to sort this out.
Steam needs the ok from 1C to set up the separate subfolder in ..\steamapps for both AP and CW to fix this problem.
You have an issue as well - but haven't noticed it either because you haven't noticed it (the game launches, the data is wrong) or because you haven't tried to run or verify the game cache files for AP since installing crossworlds.
If you try to, you will reacquire a number of game files
I've documented elsewhere.