I think that the upgrades should stay on your vehicle through out the game, then just pile on more upgrades. It's disappointing when your upgrades get reset back to nothing.
The new vehicles actually come with all of the previous upgrades, there's just more to get at that point. Upgrades go from 0-9 from a program code perspective.
 "QuackTheDuck"){kind=icon}
 "Evolution vs 1000 kittens"){kind=icon}
 "Spam defender"){kind=icon}
 "Snowbowl"){kind=icon}
 "Vector Boom"){kind=icon}
 "Crystallis Navigator"){kind=icon}
 "Vampire Physics"){kind=icon}
 "This is the Only Level"){kind=icon}
 "Violet Sky"){kind=icon}
 "Blood Red"){kind=icon}
 "Commie Crush"){kind=icon}
 "Six"){kind=icon}
 "Fractured"){kind=icon}
 "Piano Talents II"){kind=icon}
 "Japanese Kana Drill"){kind=icon}
 "Medical School"){kind=icon}
 "MusicQuest Pro"){kind=icon}
 "Gateway II"){kind=icon}
 "Record Tripping"){kind=icon}
The new vehicles actually come with all of the previous upgrades, there's just more to get at that point. Upgrades go from 0-9 from a program code perspective.