So in an effort to reduce Draw Calls we're using combine children on a large number of objects when they are not in use or being interacted with. We're dividing these objects into groups and combining the children within those groups.
Would it be possible to reverse the operation should an interaction be needed?
It should be noted we're doing this in real time, hence why we divide into groups to improve performance. If there is an interaction needed, the game would look to the group nearest the player and "uncombine" it as needed.
Assuming you have the good objects as children of a parent, then run CombineChildren on it.
Look in the hierarchy and you will see that those objects still exist. They have their renderers turned off. So what you can do now is turn off the parent renderer and turn on the children.
Colliders on the children never turn off, unless the object is made not active, or you delete them. So even with all the children combined you can click on objects and the scripts will react.
If you add a collider to the new parent and keep the children active the colliders will conflict with each other.