You could try an Account Reset under Account Details for the problem account. But sometimes when I have received that message, it required that I deactivate all accounts from that FI and then use to Tools>Add Account to LINK the accounts back to the appropriate register accounts.
Then try deactivating all of the accounts at the FI. Then use Tools>Add Account to LINK your existing registers with the accounts found online. All of your old transactions will be preserved. By deactivating all accounts (including any old hidden accounts) you will start with a new profile for that FI that should resolve your ongoing issue.