Maybe... now,,, I had this problem once last year...
When I've done a auto build & program in MPLabxIDE, I accidentally disconnected the PICkit3 from my 6 pin sip header in the middle of programming. MPlab did report an error, but after reconnecting the pickit3 and trying to program again, it failed to see my Pickit3, even after closing MPlab and disconnecting the Pickit USB cable and reconnecting. The way to get it working again was I found in my task manager/processes a second microchip Mplab task frozen there in the background. After killing it, everything worked again. Now, I've accidentally disconnected my programmer a number of times without it affecting MPlab, this 1 time was a fluke chance, but if you have another frozen microchip programmer process, which looked like you closed it, but it is still running as a frozen service in the background, it needs to be 'End Process' before the programmer will work again, or, just do a reboot to clean everything.
Note that I was using Win 7 professional 64bit.