basically, you're trying to form a "wide" connection (with x8 bandwidth) between your controller and the ports served by the first expander. is there any setting on the controller related to "wide" negotiation? does it behave the same if you connect both x4 links to the expander for the top 24 ports? (ie, the "HBA2" connectors)
connecting the controller to one x4 connector for HBA1 and HBA2 would logically cause the controller to negotiate two narrow links (to the two expanders). (but that's how you'd use that one controller to connect to all 48 front bays.) I speculate that the renegotiation made the controller firmware think the disk setup had changed as well - so it doesn't want to treat the disks as already-configured.
I'm assuming you have the "non-cascading" expander architecture.