Reproduction steps:
1. Open the attached project
2. Select the cube in the hierarchy
3. Check any two of the "freeze rotation" parameters in the rigidbody component
4. Hit apply on the prefab
5. Observe the parameters reset instantly.

note1 This doesn't happen when all three parameters are set to true
note2 If you drag an other instance of the prefab into the scene, the parameters seem to be fine (they're set to whatever's been set to them)

Reproduced on: 5.5.0b11
Not reproducible on: