Why did changing the receipt application reverse an adjustment?

Because transaction adjustments created after receipt application no longer apply when you change the receipt.

For example, you apply a $99 receipt to a $100 invoice, then you adjust the remaining $1 to close the transaction. If you later change the receipt application, either by unapplying the receipt, reversing the receipt, or changing the applied amount on the receipt, this reverses the adjustment on the transaction.

If necessary, you can retain the original adjustment record by creating a new adjustment in the transaction or in receipt details.