Reversing a cheque is a 2-step process as you've discovered. First the BR module, then AP module.

It can be made simpler by configuring your Bank in the BR module. Edit the Bank, go to the "Interface" tab and under "Update Payables Check Reconciliation", select "Pending Status".

Now when you Reverse a cheque in BR, the cheque in AP will automatically be marked as "O->R". You still have to go to AP and post the Check Reconciliation but it's easier.

Note that the act of Clearing a cheque in BR will now also update the status of the cheque in AP.

Hopefully a future version of Bank Rec. will perform this function in one step.