Old thread, but I'll add some advice for anyone finding this in the future.
The easiest option is often to park the vehicle between the borders. I was in Costa Rica 3 months, went down to Panama for a couple of weeks, then came back. Costa Rica wouldn't let the bike back in (after 90 days in CR a vehicle has to be out for 90) so I wandered around the border town and parked the bike in a fella's front yard. It's covered and fenced in all round. Then I got on a bus into Costa Rica.
Otherwise, if you leave the vehicle inside the country, you have to be back by the time your vehicle permit expires or you'll get into shit trying to leave with the vehicle.
Love & joy - Callum