Comment by stavros

Shorting almost any two of the communication lines of the flash chip will corrupt the communication enough that the ethernet controller thinks there's no flash installed at all.

I have no idea about S0 but CS is usually chip select. It should be sufficient to short it to prevent the chip from being selected. However CS is frequently inverted and you would have to pull it up to prevent the chip selection, so maybe S0 is always high and inhibit CS