On your board it seems there is no way to disconnect the EEPROM physically either using a switch or something.
1. I think the device is not binded properly with the drivers. Please check if there is any warning mark on the side of the device in device manager. If so. then manually bind the drivers . please refer the link http://www.cypress.com/?app=forum&id=167&rID=97312
Once if the drivers are properly binded then you can see the device in control centre.Now you can reprogram the RAM/EEPROM.
2. Cyconsole doesnot recognize the device if the device is not binded properly with cysub/cyusb3 drivers.