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"I was told NOT to delete these transactions even if they are duplicates because it will mess up everything in the books, however these duplicate transactions are messing up the books by keeping them because the statement ending balance and the register balance for each month of the reconciliations report is off by these old duplicate transactions."
You're correct that you do not want to delete them. Every entry that you see in the reconciliation window has a corresponding and equal entry to an offsetting account. So, for example, if you have a check for $500 that is listed in the reconciliation window, there is an offsetting $500 entry to an expense, asset, or liability account. Those entries were all used to report the previous year's tax returns. If they are duplicates (errors), that means those errors were reported on those tax returns. Therefore, you need to reverse those entries in 2023 (offset deposits with checks assigned to the same account as the duplicate deposit and checks with deposits assigned to the same account as the duplicate checks) and clear them against each other.
