we had a german shepherd who had this problem and wasn't digesting her food properly so was way underweight and after many tests and a few vets it was diagnosed as pancreatitis - a problem in that the pancreas doesn't produce the right enzymes to digest the food. There is an over the counter product called ProZyme but that wasn't enough for her, so we special ordered a prescription enzyme, but I can't remember the name now as it's been a few years.
This had to be put on any food she ate so she'd be fine, unless she got into something she shouldn't have (like a box of cereal)
It literally took months for this to be diagnosed, so if your vet hasn't tested or mentioned this, it's worth a shot.
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