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Select AT90USB1286, get ATMEGA32U4 and missing pins in schematic
I loaded a layout from KLE, selected AT90USB1286 to get more pins. The new pins are available to select in the Pins tab. Saving the config and reloading it does restore the AT90USB1286 selection. However the generated PCB layout contains a ATMEGA32U4 and the last few columns of the matrix are just not connected to the microcontroller.