Alright here is what I've found.. I experienced this myself and needless to say.. it sucked. Rockstar acknowledges this as a bug and are working to fix it.http://support.rockstargames.com/hc/...osing-upgrades
While we wait I can recommend that you never drive a car to a mission, it will most likely disappear. The impound lot also seems sketchy at best, sometimes it will impound random stolen cars for me overwriting one of the two slots(erasing a pimped out car).
So basically drive your car out of the garage... and then when you are done drive it back in(Freeroam fuckery is still a bit of a risk if you get killed or have to switch cars to dodge the cops because of the buggy impound lot). Pretty bullshit on rockstar's part.. Seems like a bug you would find within a few hours of gameplay the first time you take your very first ride to a mission. I doubt we will we get a patch before GTA:O.. but who knows.