The PROGRAMN pin does not affect the JTAG state machine or boundary scan cells. However, the PROGRAMN pin does clear the SRAM configuration memory of the device.
Because of this, a logic low signal on PROGRAMN pin at any time during JTAG configuration process may result in a failure due to the SRAM cells being cleared independent of the configuration process. Therefore it is important that the PROGRAMN pin is held at logic high during the configuration process.