Slvrsrfr Hey! The Cosmoteer standalone version is definitely still available, and will be until the full V1.0 release, upon which point it will likely move completely to steam for workshop integration among other things.
As far as where your saves and stuff went, player data is stored at Documents/My Games/Cosmoteer. If you switched users on this computer it could explain things, since each user has their own Documents folder (therefore switching users creates a new "set" of save data). If the entire game is missing though, I'm not as sure what could have happened. You can check (by default) C:\Program Files\Cosmoteer to see if the standalone version of Cosmoteer is currently installed. If both that folder and your save data folder are completely missing, my only real guess is something external deleted it, like a different user, a 3rd-party uninstaller program, or an OS reinstall or something.