YAY! That's great!
He will be a bit slow for a while, but should get his energy back soon. If you give him some high-protein foods, like Daphnia or Bloodworms (Live, Frozen, or Freeze-dried), that should help him perk up a bit.
Oh, and you might want to continue treating the tank he is in, just to make sure there are no eggs that hatch and start your problem all over again.

Edit: Just saw your edit! Yes, you probably killed most of the bacteria. I'm going to say it probably would be the same either way. Both aren't cycled anymore...
The fish you have are generally pretty hardy, except for the Neon, so they will probably survive the cycling. You can also use a product called Bio-Spira to help speed the cycling.
Any tanks that are mature that you can take gravel, or filters from?
He will be a bit slow for a while, but should get his energy back soon. If you give him some high-protein foods, like Daphnia or Bloodworms (Live, Frozen, or Freeze-dried), that should help him perk up a bit.
Oh, and you might want to continue treating the tank he is in, just to make sure there are no eggs that hatch and start your problem all over again.

Edit: Just saw your edit! Yes, you probably killed most of the bacteria. I'm going to say it probably would be the same either way. Both aren't cycled anymore...
The fish you have are generally pretty hardy, except for the Neon, so they will probably survive the cycling. You can also use a product called Bio-Spira to help speed the cycling.
Any tanks that are mature that you can take gravel, or filters from?