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That is VERY weird! You should be able to prevent the issue by getting it back to AWD, and the disconnect the harness connector from the shift motor. The Gen 1's used a TCCM, but I believe the shift commands come from a different source for the Gen 2 D's. Simply doing a drain and refill on the trans should not have any effect on the transfer case.
Did you replace both filters inside the pan?

Don
 
It's been a while since I've been under mine, but I believe there is only one connector on the T case. When you remove the connector, be sure to secure it up and away from the driveshafts so it won't get damaged. Your Service 4wd light will come one, but that is due to the connector being apart.

Don
 
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