If you had to rebuild the transmission, then you should have the transfer case rebuilt too. Whatever happened to the tranny affects the transfer case.
Yes and no. The only thing physically related between the two is the output shaft of the transmission. They do not share fluid. If they do, you have a seal leak which does happen. Other than that, the operation of the transfer case may depend on a whole host of other things such as transmission gear selected, engine parameters, vehicle speed, front propeller shaft/rear propeller shaft speeds etc etc etc.
I'd say the transfer case fluid should have been drained, refilled, and checked for proper operation, but if the adapter was dry inside as the transfer case was removed, there is no danger of transmission fluid having infiltrated the transfer case. What Jack should have done is have the TC pump modification done to prevent case wear. But, given that a transfer case rebuild could very well have added a good thousand to the repair cost, I can understand why Jack did not yet have the TC rebuilt.
Jack, I would immediately check the fluid level in your transfer case, and look for any leaks from the case. You can search this forum to see where the wear points are in the TC so you know what to look for.