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If you check the API guide/comments just before the CyU3PUartSetTimeout() API, you will see this note:
"The API keeps the CPU spinning until the data transfer is completed, or the specified timeout period has elapsed. Therefore, it is not desirable to set a very large timeout for these operations."
It is not advisable to use this API with large timeout. One way to do this is to have a less timeout in CyU3PUartSetTimeout() API (Assume 10ms instead of 1 sec) and then do a CyU3PUartTransmitBytes/CyU3PUartReceiveBytes. If the API times out call CyU3PThreadSleep(10) and retry. This way your normal video stream won't stop.
Please check if it helps.
Thanks for your reply. I will try this and get back to you.
Ashlin Surey. A