I'd simply remove the XML file from the microSD and see if GE complains when you next try to update the map and software. Going by your earlier posts you're not using the original card to which the XML belongs anyway so i can't see that there'd be any problem.

As to the unit not wanting to disconnect in MSM, that is NOT proper behaviour for a 3597, with or without a card. Some units such as 1xxx and 7xx series will reboot and run in navigation mode if not immediately disconnected from the PC when safely removed, but my 3597 simply turns off as do other nuvi series.