The following pins are not used in the software packages:

PinPin numberDirectionType
AVR_RXDAW35INLVCMOS25
AVR_TXDAY34OUTLVCMOS25
E_KEY0_FPGAD15INOUTLVCMOS25
E_KEY1_FPGAC15INOUTLVCMOS25
E_KEY2_FPGAG12INOUTLVCMOS25
E_KEY3_FPGAH13INOUTLVCMOS25
CUSTOM0_FPGA_IOF15OUTLVCMOS25
CUSTOM1_FPGA_IOAW16OUTLVCMOS25

AVR_RXD and AVR_TXD are UART links RX and TX between the FPGA and the AVR.
The other pins are either GPIO pins or a SPI link between the FPGA and the AVR. There is also no code on the AVR that uses these pins.