To add a data point:
I am currently trying to change FFN in my upcoming DONE3 from BA to AY and it is quite a task...
All Amadeus airlines were easy to change, only noticable things so far are lost seat selection on JL domestic (apparently my original seat row is only availble for elites) and on trans-atlantic IB sector.

For AA flights had to call them as their website would not keep my added (new) number after they had removed the old number.

Same for AS flights, when calling guy says he now sees 2 numbers in the system but was able to remove the old one (again their website did not offer to change FFN at all).
This I still need to check, it is still in the what I call "cool down / sync phase"

Ergo:
If you want to swap number be prepared for multiple rounds with agents, double (better triple) check and do it all well in advance your journey so all the backend systems / databases / whatever have enough time to sync...