Part Number: 66AK2H12
Tool/software: Code Composer Studio
XDCtools 3.32, SYS/BIOS 6.46, CCS 7.4, PDK 4.0.7, NDK 2.25, IPC 3.46.2.04
I have exactly this problem:

I am using GIT integration. After making project changes, excluding a folder and a file and changing some gcc compiler symbols, I close CCS. I can see the updates in the .cprojects. The are seen in GIT GUI. (I do not commit or save or anything - I just tried using GIT GUI as a tool to see if the .cproject was modified then exit GIT GUI). When I re-open CCS, the changes are gone. Exit CCS again and take another look at .cproject and the changes are indeed reverted. PITA! I'm 'lucky' in that if these changes don't get recalled, compiles fail. If not, and the projects compiled it could be very bad; introducing unintended operation.
Is there a work around or fix?
Mike