As per your description "And we replaced the evaluation board components to our customized board it's working quite good.", may I understanding the device CYPD3125 on CY4531 can working well on your board, but the all new CYPD3125 can not work at all? If my understanding is correct, the next step you need do is program the firmware of CY4531 into the device on your board.
The firmware project of CY4531 can be get it from the link: https://www.cypress.com/documentation/software-and-drivers/ez-pd-host-software-development-kit
After you install the SDK, you could new project with example project CYPD3125-40LQXI_notebook and build it. You will get HEX files of the project.
If you just want to confirm whether the HEX file could process this issue, attached HEX file for your testing.