i was always under the impression not to use live rock or sand or anything that could soak up medications you may use, i know water parameters are a must as well as water changes. a quarantine tank could be used maybe with a little something depending on what your using for meds, but in a hospital tank id keep it to the basics but i would try to let the hospital tank run for a few days or a week to let things "even out" . all the things you use in a hospital tank need to be cleaned constantly , like a human hospital your not wanting to add any more bad bacteria. get some water tests done and if anything shows change some out with new saltwater , dont do it in a hurry to stress the fish more do it in small amounts where the fish barely knows your doing it
also losing two fish doesnt mean your meds arent working or your methods are flawed could possibly mean two accounts of bad luck, alot of fish dont make it through punishment like losing fins while alot of others do , it could be the timing
interesting read though on the link you posted but i would imagine that theres always going to be a stradnd of bacteria we cant treat for, so its best to treat for what we know we dont want