Agreed with Ballypinball 's advice, unplug the playfield at the rear connector panel before you do that. The coil/switch mappings are different between the games (particularly the SW:E1 magnet that has longer pulse times), so that'll keep you from burning something up.

Otherwise, there is no reason you shouldn't be able to swap the PRISM cards. Toss the SW:E1 PRISM into your RFM after disconnecting the playfield, and that'll tell you if its the PRISM or something else on the other computer. Feel free to post what else you're seeing with the other computer and we'll try to help.