I'm not sure Restructure was meant for mass moving of components from one assembly to another in the assembly hierarchy... Keep in mind that as components are relocated from Assy-A to Assy-B, that the assy-constraints for that component still reference geoemtry from Assy-A. You are, in fact building layers of external references from Assy-A, through the Top-Level Assembly and finally into Assy-B.
This can create very nasty situations later when you may want to open or check-out just Assy-B, but of course Assy-A and the Top-Level Assembly are required for it to regenerate.
As a matter of practice, I always 'package' any component before I restructure it. Then I either re-create the constraints in the new assembly, or use the 'fix' constraint. That way there is no external reference baggage brought along for the ride.
If you need to move a bunch of related components from one assy to another, consider creating a UDF consisting of all these components and then applying that UDF to the target assembly... This method works pretty well as long as there were few assembly references required to assemble the components into the source assy (other than any references they have to each other - which will not be required for UDF creation).
-Brian