I just learned this again (finished story mode in 2013 and forgot). If you do not move your saved vehicles out of Trevor's La Puerta garage (Wade's house actually) before the heist missions on Humane Labs and where Trevor kidnaps Patricia Madrazo, the cars there will be gone forever.
I just paid $30,000 for a garage to move this special NPC customized car to that I had stored at Wade's house garage, I go there.....it's gone. I reload the last save file.....still gone. I think it's when Trevor tells the O'neil brothers to come get him in La Puerta. It's when "Hang Ten" mission starts.