Thank you for taking the time to visit the Community to post your issue, although I apologize that you haven't received a response.
To answer your question, marking as done would enter an adjustment. An adjustment may be created if the difference isn't zero, but you don't wish to spend time to resolve it, Quicken can record an adjustment transaction in your register balance to make it agree with the bank's balance.
To learn more about reconciling and adjustments, please see the support article here.
I hope this helps!