Repair/rebuild resets PhpStorm's favorites

I believe SalesAgility devs used to use PhpStorm so hopefully someone knows the answer to this. Basically whenever I do repair and rebuild it resets all of the favorites in PhpStorm. The favorites are stored in .idea/workspace.xml, so i’m not sure how or why repair/rebuild operation affects it.

Has anyone been able to fix this? Is there a way to possibly force repair/rebuild operation to ignore this specific file?