If you connect a plain EEPROM (without any image file in it) to the Cy7C680-13A usb high speed controller then it enumerates and you can download the code into the RAM using CyConsole. Now if you want to program the EEPROM you can do that. Once you give the hard reset, from that point it is going to get the code from the EEPROM.
Then you should be doing two things to enumerate as a Cypress default device.
1. You should be having the firmware to support EEPROM erase functionality. You can initiate this using a vendor command.
2. you can short the SCL line to ground while you connect your board to the PC. Then it enumerates as a default device and you can re-program it.
Coming to the tools on Linux platform, I will update you ASAP.