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Buy nowHi,
Not sure if you already found your best solution.
But from what I understand, you wanted to clear all old unreconciled transactions without having to delete any old transactions, even if these are duplicates, as to avoid any adjustments in your FS balances in previous years.
What I do with other platforms, is I create an adjusting journal entry to reverse all the effects of these old unreconciled transactions, but of course not to the point that balances goes beyond normal acceptable credits or debits. If it does, I chose other GL accounts that can absorb that reversal effect.
After recording that adjusting journal entry, I redo or create a new reconciliation and include the old unreconciled transactions in that bank reconciliation as well as the adjusting journal entry.
In effect, the total deposits and payments will not match but the ending balances should match.
Moving forward, the old unreconciled transactions will not appear in the succeeding bank reconciliations.
Hope this solution helps. And any corrections to my method are very much welcome.