Changing the a model's rig "Animation Type" (to and from any) makes all child meshes of the rig that have non-uniform scale to rescale (factor unknown) in prefab instances.

Fixed by entering play mode
Only affects prefabs of the model/rig
Only effects meshes with non-uniform scale

Repro steps:

1) Open attached project and scene "Scene"
2) Select model "Character" (not prefab)
3) In Rig tab change Animation Type (to any)
4) Apply and witness mesh "Eye" recieve scale factor in the prefab currently in scene
5) Enter play mode to fix

Reproduces in 5.6.0b6
Not reproducible in 5.5.x