Yes. They keep the scryp they’ve earned and their history is maintained. If the system is later re-added, it acts as if it never left.
Reconfiguring your home cluster as an ongoing thing is totally intended and encouraged. You’re even welcome to have a rotating set of home clusters if you can’t decide on just one.
We do ask that you don’t do it in an exploitative way (e.g. by remaking simple systems repeatedly to grind for scryp).