After starting HIDBootloader.exe the main window shows
If the device is not already in boot loader mode, start bootloader by holding BOOTLOADER down while pressing RESET.
After starting bootloader mode the device will be detected automatically by the application. Now import firmware image, by loading the appropriate HEX file.
Start the Erase/Program/Verfiy process
After successful programming just reset device, to start the programmed firmware. The application will show "Device Detached" after resetting the board.
NOTE: There are 2 different versions of the utility, both showing version "USB Bootloader v2.9j", but with little difference in error handling on verify after programming. If you encounter "Verify failed" error while programming new firmware the version from 20.12.2013 should fix this.microchip_solutions_v2013-06-15\USB\Device - Bootloaders\HID\Software Windows Executable\HIDBootloader.exe (2013-06-17)