JTAG chain not seen unless factory_load switch is set

Thanks for the link. The BTS "Erase Flash" feature looks like it only erases a single sector. However, whatever configuration is used with the BTS could also be used to erase the whole flash. If the documentation includes details on the system controller memory map, you should be able to use that via JTAG to erase the flash (the max5.zip has the source, so you can figure it out if needed). However, you should also be able to follow the instructions in Appendix A of the User Guide to restore the board to its factory default state. I'll often do that step as soon as I get a board, just to ensure I have all the correct images. You can restore the MAX V system controller image too.