When I plug in a USB cable for using Control.  The pedals refusede to accept MIDI PC changes from my Joyo switcher.  Can I disable this from happening? 

No. When you connect to your H9 via USB, MIDI messages are sent thru the USB so H9 cannot recognize the messages from your switcher. You may use Bluetooth to connect to your H9 on your PC or mobile devices. This won't affect MIDI communication.