Last night my Rally arrived from amazon and despite almost all signs of any parasites having disappeared I netted the clowns out and gave them their 90 minute bath at .8 tsp per gallon. Salinity was matched and temperature was about 2 degrees higher in that water, as dialing in a temp with a last-minute cheap heater with 5 gallons of water wasn't the easiest. I normally keep my DT at 78.6 and this bath was at 79.9. This was the closest I could keep it between 81 and 78. Thank you, Aqua Top heater.
Clowns were hungry and trying to eat particles in their bath, almost making a mockery of the process.... silly fish. After 90 minutes of bath and 5 minutes of netting time, they moved from that bath in to the QT at 78.8 degrees and matching SG (1.024 to be exact), which also had a half dose of Cupramine already added, with the other half dose due 48 hours after. Fed the two clowns within 10 minutes of their arrival into the QT and they happily gobbled everything in the Rod's Food. So far, these two are real troopers.
Display will stay fallow for the next 3 months. I know that brook's fallow period is 6 weeks, or 1.5 months, but since this parasite appeared to recede rather quickly from the 2 fish and stay that way over the course of 2 days, I haven't yet ruled out the possibility of Ich, despite the first mucous-esque appearance of my one clown. Ich, having a fallow period of 72 days, urges me to round up to 90 days, to make sure NOTHING is left over! So now I let my tank finish its cycle, let my corals have a chance to mellow out for the next few months, and then I will re-acclimate the clowns.
I will update if anything changes, but since I still do not know what exactly the fish had, and still haven't gotten similar stories of brook disappearing on its own, I remain skeptical and cautious, and hope that my 2 little guys don't get too bored in their 10 gallon.
Thanks again, everyone, for your responses. If you have any experience with fish beating brook on their own accord, please let me know, as I am very curious about this. I realize this thread should have been posted in the disease section rather than tank emergency, and will post there in the future.