I just finished Reed path in both of it's ending, and I wanted to return to firestarter mission but autosave with that point is now gone.

I looked at the Saved Game folder, but it's empty, there's not even a Cyberpunk folder in it. Does anyone have any ideas how to fix it? Or do I have to start the game all over again?

For me, the saves are located in:
C:\Users\[USERNAME]\Saved Games\CD Projekt Red\Cyberpunk 2077

With currently 112 items in it.

I have read Windows 11 had some bugs related to randomly deleting user data on earlier revisions, but I would assume that's not the case there.

If your save game folder is empty, and you never made a backup, then I guess you have to start over again.