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It is always a good idea to disconnect power from the PIC before plugging in your PicKit. I would not plug it in while the chip is running its program.
PicKits often hold the devices in reset for programming. There is an item in one of the menus (program, maybe?) to release from reset. Clicking that should set your chip running again.
That was it, thankyou - theres an option to release from reset - no more unplugging after each programming!