Cmd line MPLAB via MicroCode Studio and PICkit v3.10 seems to work now OK, which is good 
But, GUI MPLAB's still seems to have some issues:
MPLAB X IPE v2.00
Target device was not found. You must connect to a target device to use PICkit 3.
MPLAB IDE (v8.92)
PK3Err0045: You must connect to a target device to use PICkit 3.
Firmware upgrades/changes were successful in both GUI environments.
In all cases I have used same HW, so that is not an issue (and yes, PIC was connected to PK3). I think issue in PICkit SW...
My PICkit 3 is real Microchip one (made in China). Same poster was in package
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