When an atom incorporates either other atoms or Free Chains into itself. It causes the Atomic Chains in question to get compressed in the parent Chain Reweaver. In the case of Free Chains can either reconnect the ends into a full Atomic Chains or just eject it out the other end after a single pass through the Chain Reweaver.
It is also possible for only some Atomic Chains in an atom to get absorbed into the parent atom. While it is very rare for a collapsed atom to tangle, when they do often only a single Atomic Chains that tangles and it can be pulled free and absorbed by the parent.