It is a while since I used the Flex 6000 but I seem to remember they are SRAM based and the programming is normally done with an EEPROM. If that is the case, it should be easy to duplicate - the data is not encrypted. It could be loaded from a device such as a microcontroller instead, which would be more tricky as that could be code protected. If you have the circuit diagram or a physical board, look for a small 8 pin EEPROM next to the Flex 6000. There would most likely be a JTAG programming connector as well.
Keith