Your skimmer will likely do that for the duration of your treatment. If you are done medicating then I'd do a hefty 50% water change. Then in two days another 25%. You should be diluted enough by then to continue regular water changes.

Yup, I would say that O2 depletion killed your fish. When the first fish died, its decomposing body would also contribute to the problem, including stress on fish that are already being stressed out by disease, lack of oxygen, etc.

An air stone and maybe extra powerheads would let you get away with no skimmer during a medication treatment.