Thanks for all the information but weve had fish for about 20 years including having dojo loaches and goldfish living together which according to other resources is perfectly fine. We have a 55 gallon tank with two filter pumps. We never change both at the same time...neither do we ever vacuum more than a third of the tank gravel per water change. We also leave two thirds of whatever decorative fixtures we have in the tank and only switch out a couple at a time. And if we do change a filter its about every six to eight weeks average. We clean the tank every ten days to two weeks average...at least when there were five fish in there. So there should be plenty of beneficial bacteria in the tank. We dont have the best water for fish anyhow as it is well water...well filtered but still. Thats why we stick with the fish we haveSorry, very long response here. TDLR at the bottom...
Changing the filters is actually one of the worst things you can do in a tank. That brown scum that builds up on your filter media? That's the beneficial bacteria that deal with your nitrogen cycle. If you had nothing but sponge in your tank, forget the charcoal and "bio-media" and all that stuff, you could have enough bacteria to maintain proper cycling in your tank without needing to change media. If the filter media gums up too badly you take half of it out and add in fresh, you never clean all the filter media at the same time. Charcoal is really only needed if you are trying to remove medications or other impurities like that, it doesn't do anything to help the cycling. And the fancy filter media with ceramic and plastic and all of that has less surface media than a proper sponge. I forget what type of sponge it is and the exact square inch ratio required. But if you're using a hook on the back (HOB) filter then those filter cartridges that they tell you to change every month are basically crashing your system every single time you swap unless you take some tank water, squeeze the old filter out into it until it gets brown and scummy, and then soak the new filter in it to seed it with beneficial bacteria.
Second, goldfish really should only live with goldfish. Introducing other fish species into the tank can introduce diseases that goldfish can be too inbred (low immune system) to withstand, stress the other fish since most are not cold-water species like goldfish, and if they're bigger than the goldfish they can maul the goldies, and if they're smaller the goldfish will try to eat literally anything they can fit in their mouth. That includes fins. On top of that goldfish put out a growth reducing hormone that builds up in the water and that can also cause distress to other fish.
I am not very familiar with the virus you're speaking of, but if you got a new tank I would just completely start over from scratch and reintroduce any new fish to the tank with a water acclimation drip from the new tank water to their old tank water, and then when properly acclimated just remove the fish from the old water and place into the new without adding any of the old tank water into the new system. Other components such as substrate and plants can be disinfected beforehand with hydrogen peroxide (for plants), or bleach solution (for other substrate/decorations) and rinsed very well.
According to once source:
There is no treatment for lymphocystis. Often, clinical signs of lymphocystis are exacerbated by other stressors in the tank, such as poor water quality, poor diet, or inappropriate temperatures.
Poor water quality is not just the nitrogen cycle. It's the levels of bacteria in the water column that you cannot see. Most of that should be taken care of by a properly functioning filter, but overcrowding and under filtering will cause imbalances. The goal is crystal clear water, not slightly hazy, but crystal clear.
TDLR: check your filtration setup, also no need to keep old water when switching to a new tank if fish are properly acclimated at a slow pace.