When I created and downloaded my original mdl file, I only had 6 "clones" out of 360 custom buttons, but in general I would start out with the Default.MDL screen for each device, and then on each screen just changed the button style then moved it a few pixels as needed to line up correctly, but rarely if ever moved buttons across each other. And I rarely inserted a button from scratch. (Only if the default screen had fewer buttons than I needed) I deleted the old text and added new as the last step. For the 6 clones, on the remote itself I deleted and reinserted each key. Then relearned it. They all worked fine after that.

I had an unrelated problem learning macros. If the macro included keys from another device, it cloned the macro to a key in the same physical position on the other device. But you can erase the macro from that key and it returns to its original learned function.