Hello,
CompactPCI does not have the synchronization backplane of PXI, as PXI builds on CompactPCI by adding synchronization, among other features. I believe you will lose the ability to synchronize on the backplane if you move the PXI modules into a CompactPCI system (though individually, the boards will work fine).
One alternative is to move the CompactPCI modules into a PXI chassis - since CompactPCI modules will also work just fine in a PXI system.
Regards,
Greg