I programmed FX3 chip with the firmware available with the design note AN65974 with small changes such as
commenting #define LOOPBACK_SHRT_ZLP
uncommenting #define STREAM_IN_OUT
But when i send data through c# application it does not update FLAGC when viewed in ChipScope Pro.
What do you mean by FLAG C not updating. By default FLAG C is used as an Empty Flag for Thread 3 . It will become empty if the external master has read the entire content of the buffer associated.
What is the status of the FLAG when you are checking it?
You can also create a Technical support case in Cypress.com.