Now the queen is crippled and has one functional leg. But, now I know what is killing them, formic acid poisoning. I put them under too much stress. In four months I moved them into five different setups. First, their test tube was dirty so I moved them into a new one, then that one got mouldy, so to the acrylic nest they went! Then I realized they were to small of a colony for it so, to the tubing setup they went! Then that got dirty, so new tubing setup! POOF! dying colony! Thanks for reading: how to kill a colony in four months!
I know it's not gonna help now but maybe it will for the future - a bit of mold is not a problem. In fact even if the entire cotton is black most of the time that isn't a problem for the ants.You can offer them a pile of sand, many ants will stick sand to the wet cotton and successfully suppress mold that way - and of course you can always offer them a new test tube and just wait. If you realize you have put you into a nest that is way too big for them don't try to pull them out of it, just offer them a new test tube - they will most likely either nest tin the tubing between the nest and the outworld or will relocate to the new test tube (may take a few days for them to discover it though).
Generally stay patient, ants usually know what they are doing and most ants can survive even under conditions that are less than perfect - many of the more dry-resistant ants (like most Camponotus species) can even survive in a corner of the outworld. If their current location is so inadequate that their survival is threatened they will search for a new one and quickly relocate when they find one.