Can I change a permanent prepayment invoice to temporary?

The classification of a prepayment invoice as permanent isn’t reversible.

So, you can’t turn a prepayment invoice to temporary after it is made permanent. However, you can cancel the prepayment invoice and create a new one for the same purpose. To do so, cancel all payment workflows before you cancel the prepayment invoice. When you create the new prepayment invoice, enable the Allow prepayment application option.