Hi Sean Mac,
There is a good chance you will be able to do this.
Especially if you are not writing to flash from your application and have not enabled block protection.
Just go through EB671 and check your code in the listed areas, should not need much trawling to do this.
On the cutback registers thing, I think you can still write to these now unused bits without any consequences and it is highly unlikely you were reading from them. Just look at table 4.2 in the GTA manual and compare this with the GB60.
Most of the changes are either additions (which don't matter as you won't be using them).
The other changes are due to the fact that a GT16 is a cut-down GB60 whereas the GT16A is more designed from the start for 16k and a lower pin-count package.
There is twice the RAM now so if your testing it you might be in trouble although maybe you can ignore what you won't use.