Thank you for taking the time to post today, dollarsanddonuts.

You can remove the checks from the print queue if you assign a check number in each of them. You can put something like EFT to indicate that they are electronic fund transfers. 

If the checks are transfers in real life, you may want to delete them and replace them with transfer transactions. However, transfers will post in both source and recipient accounts, which means you'll have to mark them as reconciled if they've been reconciled before.

Let me know if you have more questions in mind. Take care and have a good one!