The 04 FXT has the immobilizer feature? If so, you couldn't take the ROM from and flash it to a different car. Even if that is not it, what I would do is make copies of your 2 ROMs and then use a hex editor with a compare feature and compare the differences in the 2 ROMs (this will only work if they are the same revision). Then, very carefully, change the hex on ecutek map originally on the car to match all the difference on the 2nd rom. If you see a bunch of differences on the first part of the ROM, then you probably have 2 different revisions.
I'm pretty sure that ECUTEK encryption is only for their software. So, the ECUTEK software reads some bit on the ECU and if it is set for encryption will not allow the tuner to read the maps. But downloading/flashing the ROM should make no difference.