It's not clear what you mean, but it's possible we have solved a somewhat similar problem. We use a CFI complient Flash, but the Bus it is connected to on the FPGA is shared and has external bus masters. Therefore we have to request the bus before we can access flash and are not able to use the standard Avalon Tri State Bridge.
We had to write our own Flash SOPC Component to handle requesting the bus and with that are able to read/write/boot OS the Flash from the NIOS without any problems. We do get a SOPC warning that the reset address points to volatile memory as the SOPC tool does not recognize this as flash. We can also access the flash from our external bus masters as well.
However, we found that the nios2-flash-programmer does not work with this FPGA image. As a result we created a special Flash Burn FPGA image which disables all external masters and connects the Flash through the Avalon TriState Bridge. With this FPGA image nios2-flash-programmer works fine.
It's possible that you may need to do something similar.
Stefan
