Hi,
The procedure is
- Disable CleanMart temporarily;
- Upgrade VM2.x - > VM3.x
- Upgrade CleanMart to latest version
- Activate CleanMart
Yes, you will need to make the CSS changes again, because the files will be retrieved back to stock when updated. (you should have used CSS override and never touched the CleanMart core files, so you wouldn't have any single problem and upgrading would take only couple minutes, but your case is different, beside you are using RTL, it would be a real pain -- honestly if i were you, i wouldn't upgrade... VM3.x doesn't promise anything that VM2.x doesn't have -- beside better security)
Regards.