You don't need to manually transfer saves, just use the load in the new version of the game and keep playing.
I updated from v.0.4.5 to v0.5.5 and the saves are gone. can it still be restored somehow?
Saves are only carried over from version 0.4.9. and later. Replay the game, a lot has changed there) It makes sense to start from the beginning. Many of the old quests have been completely rewritten.
