Given that you are down to just a couple of fish, it might be time to do a complete stripdown/restart and run a little test at the same time. Buy some new filter pads, some filterstart / cycle / or similar, and age some water a day or two before (as much as you can reasonably store). Put the BNs in a bucket of old tank water and put it somewhere warmish for an hour whilst you completely empty your tank and filter. Wash everything (including filter) thouroughly with salty tap water (just use a handfull or two of common household salt), then take the tank outside and rinse it thoroughly. Once you are absolutely sure everything is rinsed, dry it off with a clean towel and reassemble the tank, heater and filter with new pads etc and fill with your new aged water plus a water ager if you have it. Don't put anything else in the tank (bare bottom) Toss in the filterstart and fish, and do normal waterchanges for a week or so (test for the usual signs of cycling - do a water change if anything gets too high). If everything seems OK after a week then you can probably conclude that whatever is killing your fish was in the tank and is now out; if not, then you know you have some sort of external contaminant. If all goes well then you can reintroduce gravel etc, although I'd strongly recommend you heat sterilise it (boiling water), and then new plants etc. Good luck.