I own the digital version of professor layton miracle mask. If I buy and plays the boxed retail version, will my digital version heck up? Or will it work fine? Mainly afraid of loosing my extra daily puzzle puzzles.

if it works the same as it did for FE:A, any SpotPass stuff or DLC should save to 'extra data' on the SD card, not in the game code or on a cartridge. When you pop in a brand new cartridge, it should show that you have the ability to play the puzzles and just haven't done so yet, and if you try to take your cartridge and play any DLC or SpotPass stuff on another console, that DLC/SpotPass stuff should be locked on the original console you downloaded it onto, so it won't be there on the new one. I'm not sure about things that have already been loaded into your save-file, though (e.g. if you used a SpotPass map and it put the battle point onto your FE:A game already), though, because I haven't experimented with it yet.

Anyway, that's if it works the same as FE:A, though — you may want to ask Nintendo about it just to be absolutely sure.