I don't know about the current MPLAB X version, but historically, the firmwares MPLAB X downloads to the PICkit 3 to support different PIC families, and the base PICkit 3 firmware it uses to upgrade old versions, didn't include the bootloader which made them useless for recovering a bricked PICkit 3 using an external programmer.
If that's no longer the case, it would help the community if someone familiar with the current MPLAB X would write out a cheat-sheet for locating the firmware + bootloader and re-flashing the PICkit 3 PIC24FJ256GB106.