Hi,
Actually you can do some settings in IPE so that PicKit3 can detect target voltage VDD without connecting VDD pin to 3V3 using jumper.
First, go to Settings->Advanced mode.
Log on after you have entered the password. Default password is 'microchip' as stated there.
Click Power tab on left side of the window and check Power Target Circuit from Tool. Make sure VDD is set to 3.3V as well.
Logout after you have completed the settings.
Now you should be able to upload hex file without connecting VDD pin to 3V3 using jumper. Hope it helps. Thanks.