A question about retargeting MegaWizard created items in device migration

There isn't a script to regenerate it all, but it should all occur in the back-end, i.e. just compile for CIII and it will all work. More complicated IP that significantly changes architecture, like changing a transceiver from Stratix IV to Cyclone IV, or changing a memory interface, often does have to be regenerated since options change. If this is the case, it should error out anyway. But the stuff you mentioned is pretty generic and Altera works on keeping it portable.