It would be highly unlikely that anyone would swap the trans with anything but the 47 series, either RH or RE, depending on what year it is. If you have a '99 it is a 47RE. To swap it out would require extensive electronic modifications--much more than would be economic for the usual trans shop to do, and the resulting swap wouldn't last too long because of the Cummins Torque!
It is more likely that the guy doing the service doesn't know what he is talking about. Bobalos, where exactly are you? If you are ever in L. A. area, I'll meet you and take a look at your trans if you want. I can't imagine it is anything but a 47RE. Also, I'll take you for a ride in my ATS truck! You'll like it! PM me.