AFPGA can't be programmed from SFPGA on-the-fly
We can't have direct SFPGA->AFPGA boot (SFPGA uploading the bitstream to AFPGA directly from VME) anymore as FPGA_CCLK/Flash_MISO/Flash_MOSI/Flash_CS lines can't be driven by the SFPGA anymore.
They are connected each to connected to the B1/B2 pins of the mux, which doesn't allow the B1/B2 pins to be shorted together.
Furthermore, the MODE pins of the AFPGA are driven by jumpers. The SFPGA should be able to override the boot mode and put the AFPGA in Passive Serial configuration mode in order to boot on the fly from VME.