Hi giro,
If I’m misunderstanding anything please correct me.
I believe you are talking about creating a Physics Asset? Then you are deleting the constraints and that causes the unconstrained areas to not have collision?
This is by design, when creating a physics asset the skeletal mesh should have some sort of Constraint on all of the appendages (or car doors if they are meant to fly open). You can find out more about Physics Assets here.
https://docs.unrealengine.com/latest/INT/Engine/Physics/PhAT/UserGuide/index.html
To help me understand better could you post some screenshots of exactly what you are trying to do?