How this process goes ?
I have saves for base version, not GOTY. But i don't want to start new game. So what am i suppoused to ? Should i download the base version first, to get my saves back. Or i can download them without downloading game. Or even maybe GOTY trying to pick up any saves from any version

Make sure you have backups of your saved games. Turn off cloud saving in Galaxy. Quit the game. Place your backed up saves in 'Documents'. Start the game. Turn on cloud saving. Quit the game and your saves will be backed up to the cloud (Galaxy updates cloud when you quit game).

the problem is not to upload my saves - its exatly oposite - i need to download it. I (probably) have them on old release of game, but already install GOTY edition

Well, since there no one came with any solution - i redownloaded the "old version" and ... Find there no cloud saves. Don't know why, maybe GOTY edition ovverrided it. because there no chance that i could turn off cloud saves. As well i can't understand why i have no saves on my PC. And the only reason i can suggest - GOTY edition cleaned it.
I understand that this sounds ridiculous, but i see no other ways it could happen ...

There's a simple solution: Don't rely on cloud saves. Back up manually.

Well, you are right )
But it doesn't explaine why they gone from local store