CMake is actually pretty good for this. The key part was everyone on the Windows side has to remember to run CMake before loading in the solution, and everyone on our Mac side would have to remember to run it before make.
The hardest part was as a Windows developer making sure your structural changes were in the cmakelist.txt file and not in the solution or project files as those changes would probably get lost and even if not lost would not get transferred over to the Mac side who also needed them, and the Mac guys would need to remember not to modify the make file for the same reasons.
It just requires a little thought and patience, but there will be mistakes at first. But if you are using continuous integration on both sides then these will get shook out early, and people will eventually get in the habit.