Community Discussion: Red Flag appears on Automatic Mortgage Account
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I think there are only two realistic choices: convert the loan account to a manual loan account, or delete the current online-enabled account and create a new one.
Online-enabled loan accounts do not contain loan transactions: all they ever contain is a single "loan balance transaction" which contains the loan balance as of the most recent download. [Anyone wanting to verify this can simply look at a Banking > Transaction report for the loan account.]
Online-enabled loan accounts can normally be de-activated, but never re-activated.
Given the above, there is no loss to deleting an online-enabled loan account, then re-creating it: the old loan balance transaction will be deleted when the old account is deleted, but the new loan account will contain a loan balance transaction with the newest online balance available.