The issue of using the PICkit3 programmer device with MPLAB comes down to the Programming Mode configured in the PICkit programmer device.
PICkit 3 can run in two modes: MPLAB mode and another mode used by the PICkit Software Utility (PICkit programmer Application)
When the PICkit 3 is used for the first time with the Software Utility, the device downloads an OS compatible with the programmer, then changes its operating mode from MPLAB mode to the utility software's compatible mode.
To use PICkit 3 with MPLAB IDE, the operating mode of the device has to be set to MPLAB mode.
To go back and forth between those two modes, you need to install the Software Utility ( PICkit programmer Application). This can be obtained at http://ww1.microchip.com/downloads/en/DeviceDoc/PICkit3%126.96.36.199%20Setup.zip
Once you have the software utility installed, to set the MPLAB Mode:
- Launch the software utility
- Go to the "Tools" Menu
- Click on the "Revert to MPLAB Mode" option
This will set the bootloader to run in a mode compatible with MPLAB IDE.
Similarly, to go back to the Software Utility mode:
- Launch the Software Utility (if not launched yet)
- Go to the "Tools" menu
- Click on the "Download PICkit operating system" option
Try this and let me know if you're still having the same issue