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You mean you modded a car with Franklin and you lost it? His bike will always respawn at his house, but if you modded a car and didn't store it in a garage and it's not at any impound lot (there should be a blip on the minimap to retrieve it), then it's gone forever.
I wouldn't worry about it though. You get many more chances at better cars.
What happened was I lost the car that first shows up at Simeon's dealership. I started a mission as Michael and ended it as Franklin and forgot to look for it at Micheal's house which is probably where it was. I already wound up restarting. Funny thing though. Franklin doesn't have as much ammo after restarting. Good to know the motorcycle will always respawn. Thanks for the info.