The simplest way to handle the issue would be to do the following:

In AR Manager, use the code RAP (Retainer Applied as Payment) to apply the funds to the open Invoice. Doing it this way will not have an impact on Bank Reconciliation.

Or

In AR Manager, delete the RDP and re-enter it as a PMT in AR Manager. If the RDP has gone through Deposit Processing, you will receive a message that the Bank Reconciliation program will be affected. If you were not going to re-enter the transaction as a PMT, you would need to make an adjustment in Bank Reconciliation by entering a “debit to bank” for the amount of the RDP.

When you enter/post the PMT, go into Deposit Processing and flag the entry as having been processed so it does not create an entry in Bank Reconciliation (see the article entitled Payment in Deposit Processing Window that has Already updated the Bank Balance).