Hello,
After fiddling a little with a most-vanilla save, I tried to return to my Krastorio2 game (first time I attempt this mod :D).
When I tried to "sync mods to save", I noticed that there was no Krastorio2 mod in the "to be enabled" list, but rather at the very bottom of it there were 2 entries: "Krastorio" and "Krastorio-graphics". The save is of a brand new Krastorio2 game (plus some more such as Infinite Technologies, RSO and Electronic Locomotives) so no conflict with the previous generation.