Control Center verifies when a user programs the Firmware to FX2 EEPROM. That is, after programming, Control Center checks the programmed data and source data.
For more information, you can refer to 4.8.1 LoadEEPROM on CYUSB.NET. (it is located C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\doc\SuiteUSB)
Also, source code is available on FX3 SDK web page. Kindly refer to CyFX2Device.cs if you are interested in the detail.