When you buy a tune, it locks the upgrades and tune. However, when you want to re tune a car, 90% of the time there is a glitch that occurs. When I go to upgrade my already owned twin turbos on a car it will not allow me to. The only way to fix this is to delete the car and re purchase it, meaning you have to buy all the upgrades again. When you press A to swap for twin turbos it says owned and will not install. Xbox one - ViSuaL InfamouS.
This has been around since FM3 - hopefully for FM6 it gets fixed.
To prevent this from occurring, install all possible combinations of aspiration conversions and engine conversions before downloading tunes.