Nope. You can sell one of them and you the other one should stay there. It happened to my first car and I just sold the duplicate.
Also, two good tactics for dealing with the Armored Cars online:
1. Shoot the driver, steal the truck, hide out somewhere (like in the subway tunnels) until heat dies down, then go to Ammu-nation purchase a sticky bomb and blow the doors open. If you choose to hide in the subway tunnels and already have a sticky bomb, might as well blow the doors and take the money while you're waiting for the heat to cool off.
2. If you already have a sticky bomb, you can pull up behind the truck, toss a sticky bomb on the doors, back off a little bit, blow the doors, grab the cash, and drive away to find somewhere to hide.
The first method tends to work the best. I've done it a couple times and Simply ducking into the tubes is a really easy way to lose the cops. If you take the truck to ammu-nation and blow the doors, you'll get a one star wanted level, but that's easy enough to lose.