simply hide or do not install the copy your not gonna use
to hide a game in UBI connect right click on it in UBI connect and select HIDE
i originally bought FC 3 deluxe on steam YEARS ago ..got a free copy if FAR CRY 3 deluxe as part of the far cry 5 season pass that i bought on UPLAY store as that is where i got FC 5 GOLD from
so i uninstalled my steam copy of FC 3 deluxe and only use my Uplay only one ..as its less DRM since i do not need steam open to launch my game .. just UBI connect
steam only adds more DRM to the game after all