Tuesday I woke up and didn't feel that great. It went downhill from there. I had the flu. Started taking Tamiflu that afternoon. I've also been lifting weights for the last 6 months and put on some muscle.

In 48 hours I went from 232 to 226. My calorie intake is probably around 1000 the last 2 days, but I'm still eating low carb. Do you think the weight loss is water (runny bowel movements 4x/night), muscle or fat?

In that short period of time, water loss is considerable, as your body is flushing everything. Muscle loss is unlikely. As for consumption, go with broth with electrolytes (add salt and potassium salts if necessary) and don't worry about eating, as it's usually common to wait this out by feeding your body what it needs to hydrate to continue to overcome these invaders.