When you install the legit version, the game will assign you a new id. You won't log in with your old id. You can think of them as a different entity altogether, so yes they will not linked. When I got forced-log-out a week ago, I installed the 5.2.2 mod version. Just like people of this forum had instructed, I linked my saves just fine then updated to a new version. Even if you haven't linked your account to fb yet, as long as you play the mod version, your character id won't change that's why even if you didn't link your account you could update your game with your id still.
Theoretically, if you downgraded your mod version, your game id would still be the same. I wanna try it with my another account but I'm about to go to work. Since you haven't linked your saves yet to fb, I suggest you wait for the bug to resolve first then try to link your account with your current mod version.