You need to relink your console account to your MLBTS account.
Go to your account here on theshow.com (top right)
Log out and log back in. Link your console account. You'll have to sign into the console account.
After signing into the console account, it should bring you back to your MLBTS account and prompt you to choose an account.
IDK if it will be the same for everyone, but for me, everything was saved to my MLBTS account. Just choose the one with all your stubs and levels.
From there you should be good. I closed the app on my console and everything was back when I launched it again.
This is a massive problem that SDS needs to figure out. Why did so many accounts all get unlinked at the same time? Also be sure to check that your Twitch account is still linked too. Mine wasn't.