The board has repeater code on it that, for non-P builds automatically runs at power up. P boards have no keys and do not start the repeater code on power up. The repeater code handles all the interactions to get HDMI from the 7612 to the 7511 plus EDID and HDCP processing. When AVES connects to the board it sends a STOPREP command to stop the repeater code form running. START/STOP REP buttons just sends commands to the board the enable/disable the repeater code.
If you are removing the jumpers and inserting your own BT.656 stream then the 7511 will need to be configured correctly. I've attached a script file for the 7842-7511 eval board which handle various BT.656 formats. If you examine the file the writes to address 72 are 7511 writes, you can ignore the other writes. So to get external BT.656 working you would have to
1) jumper in the BT.656 bus to the right set of 7511 pins.
2) Connect to the board with AVES
3) run the correct sequence of partial scripts from the attached file dependent on the bus width and video format.