After upgrading to Yosemite this morning I got the following error from FontExplorer X Pro:
“FontExplorer X Pro detected an unauthorized bundle modification. Please download FontExplorer X Pro again.”
If you have this issue, just download FEX again, and reinstall. Replace the old version of course and you should be good to go. Note: Be sure not to delete it using an app like AppZapper, just a simple reinstall. AppZapper will also delete preference files and the like, and you’ll lose font categories and other customizations.