No having a Discover card myself, I can't give you a specific answer to your question. Someone from Quicken would have to respond to that.
However, to avoid this problem and keep the desired full or minimum payment setting for future payments I recommend you logon directly to the biller's website (Discover) and authorize them to direct debit (aka PAC Draft, Autopay, APS, etc.) the next and all future payments from your checking account or a credit card. The biller's computer system will do all the work for you to make an electronic debit on the due date and you don't have to worry about being late.
In Quicken unlink the bill and just use a scheduled reminder which does not execute as an online payment. Record it into your account register on or before the Due Date and before you download transactions from the bank or credit card containing the payment transactions. That will allow Quicken to match your register transaction to the downloaded data and not cause any further issues.
When you update and record the manual bill reminder to the correct amount as soon as you receive email notification about a new statement being available, you will have achieved your future balance projection for the checking account.
