FORScan will definitely do it, but you will probably need an active Extended License if you don't already have one. They're free and only take a few minutes to get.
You will want to save the "as-built" data from the original GEM and then write the saved as-built file to the new GEM.
I've done at least a dozen of them, FORScan makes it pretty simple. If you run into any problems with the procedure, feel free to PM me or post back here and I can walk you through it.
1993 Ford Mustang 2.3L/5-speed, 32k
2002 Ford Ranger 3.0L/5R44E, 255k
2002 Honda CR-V AWD 2.4L/5-speed, 170k
2006 Jaguar XJ8 Vanden Plas 4.2L, 103k