Ok well i think i may have found a way. i have been experimenting with this using the laser missile upgrade at the airfield, it seems to work... yet when i put the upgrade in the command set for the individual object it is grayed out or when i click on it nothing happens. can you guys fiddle with this and see if you get the same results.
;------------------------------------------------
Behavior = ReplaceObjectUpgrade ModuleTag_28
TriggeredBy = [Entry(S) from upgrade.ini]
;FXListUpgrade = [entry from FXList.INI]
;ConflictsWith = [entry(s) from Upgrade.INI]
;RequiresAllTriggers = [Yes/No]
ReplaceObject = [Object name]
;------------------------------------------------