A number of us have invested significant time modifying our own AFCADS to match our particular traffic scenarios. It would be a shame to lose all the time and work invested in these every time a scenery is updated.
I don't see what AFCAD has anything to do with this. The only difference between an AFCAD made for SODE and an AFCAD with FSX standard jetways are...you guessed it...the jetways!
So, if you really want to edit the AFCAD yourself, what stops you from removing the FSX jetways that we remade with SODE from YOUR custom AFCAD ? This way, you can have SODE jetways AND your modifications.
The sad truth is I'm becoming afraid to buy anything that used the Couatl/esellerate engine anymore. every time I add something that uses this, I know I will have to invest time to fix whatever the new updates have broken.

What the AFCAD has anything to do with Couatl and ESPECIALLY, Esellerate ? The AFCAD is one of the few things that is entirely unrelated to them.
I think you are confusing the fact our installers, as a feature, ASK YOU if you want to download updated AFCAD, with the rest of the software support (Couatl, etc.), but they are entirely unrelated.
And, even if the installers ASK you if you want to update the AFCAD, they will ALSO do a backup of your existing AFCAD, so nothing of your eventual customization will ever be "lost".