When you void a check using the built in Void feature, it is marked cleared and so it won't show up in reconcile.  So you can do that:  Open your bank register, click on the check to void (even if you've already made it a 0.00 amount) and click Edit | Void Check from the QB menu.

Or, perform a special reconciliation where the starting and ending balances are the same, and mark off all of the 0.00 (voided) checks you don't want to see during regular reconcile and then complete the process.

Or, just check them off during the normal reconcile process and then they won't appear next time.