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I think you are mentioning about Host side applications talking to FX3 Device.
Is it a C# OR C++ application?
Howmany endpoints does the Device has? If we call two threads as Thread1 and Therad2, Thread1 and Thread2 perform read/write transfers to IN/OUT endpoints. Please provide details.
What is the timeout for the XferData() given in both the threads? Does the XferData() calls in both the threads happen independently without any synchronization between them i.e Does one thread make XferData() call only after the other thread completes doing so?
If you have given timeout as zero for any XferData call, please try giving non-zero value.
We do not have any Cypress multithreaded application.
And which driver/library(C#/CPP) are you using (Please use latest release available in FX3 SDK)