This forum is used for Photoshop bug reporting & feature requests.
I can't speak for Illustrator directly, but I'd guess they have similar guidance as Photoshop.
CS5 should run fine on Yosemite, however, CS6 wasn’t designed nor extensively tested to run on this new OS. I don't recommend that customers upgrade to Yosemite without doing their own testing to ensure that it will work for their needs with their current hardware and drivers.
If it's not obvious, you should never upgrade your critical production environment before testing. Always use a separate partition or drive.
I also recommend that you do a clean install of the OS and your software.
If it's a specific folder that is problematic, I suspect a permissions issue. Try creating a new Admin user account and run Illustrator from the new user account to see if the problem goes away: http://blogs.adobe.com/crawlspace/201...