i restored my data using checkpoint (homebrewed 3ds) and before I backed up my data to checkpoint I linked happy home designer, and used that backup to restore my data.
If you have already linked Happy Home Designer than you will get the bonuses, the game just checks if you have save data. This gives you some extra catalog items. Thats the only perk, check your catalog and if you have the "giant" items than your linked! If you start a new town I believe you will need to link it again but otherwise it stays no matter what happens to the HHD save.