Thank you for your detailed response! I may be misunderstanding your comment, but it seems the solutions you've provided are for when deposits are simply being duplicated. As shown in my screenshots Quickbooks is "duplicating" the deposit, but making the "duplicate" a payment as opposed to another deposit.

For example:

Everything's exactly the same aside from the amount being put under the "Payment" column instead of the "Deposit" column, as well as the reconciliation status shows the actual deposit as "Cleared - Tentatively reconciled" while the "duplicate" payment transaction has no reconciliation status.

I hope this makes sense!