I have Quality Turret Reworked (https://mods.factorio.com/mod/quality-turrets-reworked) installed, and when a turret is upgraded, it gets unlinked from the connected FCC (ie. the FCC will act as if that turret does not exist, despite that there is a proper circuit connection and the circuit condition is preserved). Currently the only way to resolve the issue is to remove and place the turret again (interestingly, placing FCC again doesn't help). Please see if you can have this problem repaired.

After taking a short look into the sources of the other mod, I think the problem has its origin in the way it handles the upgrade - it replaces the existing turret by a new one with the new quality. Fortunately it raises an event when doing that and it should be possible to react to this event.

V 1.2.12 which adds the missed compatibility is online