YAY! I've been wondering how he was doing, SO happy that things are looking up for the poor little guy!
Okay. . . there are several points that I'd like you to look into, so get ready for one of my infamous novels - and bear in mind that I'm not an expert, so do your own research and do what you feel is right. . .
Personally. . . once he's gone through his treatment, provided that he is behaving normally and seems to be healing well, I would go ahead and put him back into the main tank. . . but that's a tricky question, and based ONLY on my limited experience.
We do NOT know exactly what is/was wrong with him, or if it is something that could possibly be passed onto the fish in the tank. There are many people who feel that snails should be kept in their own species-only environments as a general rule. . .
That said. . . the reason why I
would choose to put him back into the main tank is because I have found Mystery snails to be extremely sensitive to changes in parameter. In my experience, they are surprisingly intolerant of changes in the nitrAte levels of the tank. If the 3g QT tank that he's living in is uncycled, he's in danger unless you're keeping a very close eye on parameters adn doing very frequent water changes. I know it sounds silly - ONE snail in 3 gallons, right? But I'm basing this on personal experience. Snails are weird little guys! Even in a 3 gallon tank with pristine water conditions, I have found that they tend to go inactive and/or float after a short period of time. I know that people keep them (fairly successfully, I guess?) with betta in very small tanks, but in my experience, they do much better in larger bodies of water!
I would do several small water changes in his 3 gallon tank using dirty tank water from the other tank, just to get him acclimated to the nitrate levels in there (if they aren't identical) because going from 0 even to 10ppm of nitrate suddenly really can shock a Mystery snail!
On the same line of thinking, you mentioned that he goes inactive for a while after you do water changes. I don't know how you run your tank(s), what the levels are, or how large the changes you do are. But if you're keeping a Mystery snail, their sensitivity is something to be aware of. Smaller, more frequent changes are better, as less flux in nitrates will be likely to happen this way. Of course, your plants are thriving, so your nitrates are probably very low - just putting the info out there JIC you didn't know :)
A few other things, while we're on the subject. . . Mystery snails are one of my favorite types of snail, and because
of this, I don't keep them anymore. These snails naturally live in cooler temperatures, and though they will survive for some time in the warmer temps of our tropical tanks, the heat increases their metabolism, makes them more active (and fun to watch!), but also has the very sad side-effect of shortening their life span to about half of what it would normally be in cooler temps. For all *I* know, you have a cool-water tank - so again, just passing along information that I have learned and read during the time I was keeping them.
I hope your little friend makes a full recovery, and lives a long and happy life with you. They really are wonderful little creatures. I miss mine dearly. . . Best of luck, and keep me posted, please!