Okay, there is an easy way, and a hard way.
Hard way first:
Go into the programming of the DKSC card :
System/Controller/Digital Endpoint Interfaces/DEI#(whichever interface)/Bay(whichever card the phone is on).
Find the extension circuits for both phones you are swapping around. Change the value of that circuit to NONE. That will kill the phone, but not kill the Voice Mailbox. Then, recreate the extension at its new circuit. You will get a conflict warning that the mailbox already exists, do you want to associate it with the extension? Answer yes, and the mailbox will now match the correct user.
But that's too stinking hard!
Slightly easier method:
Swap crossconnects of the phones back at the MDF. The phones come up at their new locations, not settings need to be changed or recreated.
But that's still too hard! You have to get up from your desk!
Easiest method. From a phone that is flagged as an Administrator: Dial 9932 (System Programming default code), dial 2, 4, 2, to get into Extension Swap. Dial the first extension to swap, press #. Dial the next extension to swap, press #. Beep! Extensions swapped! Voice mails match, buttons stay the same, forwarding paths stay the same.
Since you already changed extension numbers and names, I would suggest to change them back, then do the swap. That should get you exactly what you want