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When the large EEPROM is programmed with a firmware that does not have a vendor interface ( binding to CYUSB3 driver ), the Control Center cannot access the device. In order to recover the device, a small EEPROM (single byte address) with 8 bytes of data starting with 0xC0 can be connected on the I2C bus with its address lines set to 000. This would enumerate the device which can be bound to CYUSB3 driver and the large EEPROM can be updated therafter.
In order to avoid this procedure in the future, implement an additional vendor interface on the device. Define a custom vendor command to send data to the large EEPROM to reprogram it.