How do I break the chain?

I'm not sure I can answer your question. Your game is pretty complex, and while switching to hierarchies has probably made things a bit cleaner and more organized, it's still a complex system.

All I can do is share how I would probably approach this task:

1. Pick all moleks that are still in the hierarchy (i.e. children of Chemic). First, set attached = false for all of them.
2. For each molek in the hierarchy that is directly overlapping (touching) Chemic: set attached = true.
3. For each molek in the hierarchy with attached=false: check if it’s overlapping another molek with attached=true. If so, change its attached to true. (You might need to use a family: “Molek is overlapping MolekFamily.”)
4. Repeat previous step until none such moleks left.
5. Any remaining moleks in the hierarchy that still have attached=false at this point have broken off from the chain. Remove them from the hierarchy and launch them away.

This helps. How would Step 3 look like?

You'll need to add Molek sprite to a family, and move instance variables from the sprite to the family level.

Then you will be able to pick both in the same event, something like this:

Chemic pick children Molek
Chemic pick children MolekFamily

 Molek is attached
 MolekFamily is NOT attached
 Molek overlapping MolekFamily 
 ----> MolekFamily set attached to true