Handfeeding is actually very good to help bonding with a pup, but I know what you mean about not wanting it to be a habit. I personally don't feed canned food. Mine eats homemade stew, raw and kibble. Perhaps, take away for a very short period (say, 20-30 min) and put it back and see if he'll eat it? It could be that he just isn't hungry and saving it for later (hopefully).
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