Opinions - What is the best Process?

Current setup is H2D with dual AMS 2. Both AMS units are full and each slot has a different color filament.

I develop and multi-color model in Fusion. I then bring that model to Bambu Studio via .3mf

All is good at this point. I then slice the model and the system returns a suggestion to move one filament reel (color X) to the other AMS unit. Being AMS 2 is full it becomes a swap. color X for color Y.

What is the best process to execute this swap? As what seems to be a simple request, turns out to be more than just a click swap, send configuration to the printer.

Or am I missing something? Any help on the best way to do this would be much appreciated.

It sounds like you are slicing with the filament saving mode which does neccessitate a manual filament swap before starting the print.
Alternatively, you can slice using the convenience mode.