Hi. The cluster as a whole does not move. Only the scans inside it move. My reference scan stays fixed. I have seen rare occasions where a top down registration will move a reference scan ever so slightly, but never when doing cloud to cloud.
To hopefully better summarize -
I register 1-20 in Cluster1. Then I create a new Cluster2 and move scan 20 from Cluster1 into this new Cluster2.
I then make scan 20 my reference scan in Cluster2 and register scans 21-40 to scan 20.
Once completed, I move all scans into a single Cluster and export.
Btw, it sounds like you are doing something similar.