The Acro Naze32 Rev 6 and Afro Mini Naze32 flight controllers have no diode/mosfet circuit to prevent power from the USB port being fed back to your input DC-DC converter or speed controller, this can cause issues when you want to calibrate ESC or to program them.
The easiest way to fix this is to put a schottky diode between the two as illustrated in this schematic:
The VIN would come from your 5V regulator/DC-DC and the LOAD is your NAZE32 rev6
Any 20V 1A diode like 1N5819 1N5817 will work. Here are the Schottky Diodes 20V 1A 1N5817 from Amazon.