He has probably been drinking the whole time if he hasn't been in withdrawal. You don't have to drink copious amounts either, necessarily - to keep withdrawal at bay, a steady flow of alcohol, maybe not even enough to get drunk can keep them at bay (for some). Plus he probably has a tolerance to alcohol now, so while he might be able to drink a flask of alcohol with no outward signs of being drunk, if you drank the same amount you might be quite drunk.
The alcohol you have found may not be the only alcohol he has had. He could be drinking on the way home from work, at work at lunch, after work, no way to tell.
As for his medical issues, it's just impossible to say really.
We have done blood tests which showed he had very high ferritin and his symptoms did fit liver issues .... so I thought maybe haemacromatosis and all different things. The liver specialist told me alcohol is the likely cause of the elevated ferritin but I said wel that can't be because he doesn't drink really at all!