I lost the ATV and tried resetting the vehicle but it doesn't re appear at the base. In my opinion I think the ATV should automatically apply the handbrake whenever hopping off or at least have the option in game settings because of how annoying this is.
I also randomly got stuck in a tree running around to find the damn thing so there might be an issue with tree hitboxes too. Luckily I closed the game before I got soft locked with an auto save.