Balance History Missing on a Certain Period, Now I See Duplicate Accounts

The Balances template tries to group your accounts based on the Account Id (the Balance Id is not important in this context).

You might try the Repair Balance History workflow in the Tiller Community Solutions add-on.

If that doesn’t full resolve the problem, manually create a filter on the account (maybe using the Account # column) and manually copy the newest/current Account Id into all of the rows. This should resolve your issue.