I know that this is an old thread, but I have just encountered this exact problem in 4.13.2.
We have a child character class that is derived from our parent character class. We can change the Collision settings for the character mesh to custom, compile, save, submit to source control, then close and reopen the project and the Collision is reset to default.
This appears to be related to this issue: Editable Blueprint values keep resetting - Blueprint - Unreal Engine Forums
Our current workaround is to change the default CharacterMesh collision preset to our desired values. (Edit>Project Settings>Engine>Collision>Preset>CharacterMesh & then Edit)