First, a disclaimer: I have never programmed a PRI on a DK system, before. I started working with Toshiba on the Strata CTX line. I have worked on DK systems, but not one with a PRI.
Based on the DK manual, you do not want to change program 16. Prgm *41 appears to be for a T1 RDTU card, not a PRI RPTU. Prgm *42 applies to both cards.
I would think that if you disconnect one of the PRI cards, that the other one will automatically handle all incoming and outgoing calls. This is assuming that both PRIs are in the same trunk group in the system, and the didn't split the DIDs for some odd reason. I am not 100% sure if you can setup 2 PRIs into the same outgoing line group, but I am pretty sure that if one PRI is down, outgoing calls should route to the working PRI. This would also assume that both PRIs were setup for both incoming and outgoing calls.
I mean as a test you could unplug one of the PRIs before the cut and test all inbound and outbound calling. Just don't disconnect the one that is the primary clock source per prgm *42. This should be the card with a flashing LED.