As bienchen said, just move them to the household inventory while you move or rebuild the house. Make you sure you harvest them before you move them in the household inventory, or else you'll have to sell all the harvest from there (which is super annoying).
Drawing a room around the garden may not work very well, as the game has a tendency to move or delete things if you draw a room around them. It would be safer to build a separate room and then move all the plants into it. You also need medium or high walls if you have trees. They'll just disappear with short walls.
In your case though, disappearing probably means they'll get moved to the household inventory.