Read flash attached to Max II in Parallel Flash Configuration on legacy system

Ah, I see what you mean now. If your goal is simply to recover the binary contents of the flash, I believe the suggestion from the FAE was to use a custom IP in the CPLD to read the data out.

As for me, I would probably lean toward physically removing the flash chip and using a third-party programmer to extract its contents directly. Of course, one would need to pay attention to things like endianness conversion, if applicable.

If the flash is in a BGA package, this could be more challenging — but from what I understand, some flash programmers are capable of handling this, though it may require reballing the device before programming.