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When I run the USBBulkSourceSink example and try to get the FX3 to switch back to the 2 stage booter by calling the function CyU3PUsbJumpBackToBooter the function returns with CY_U3P_ERROR_OPERN_DISABLED and according to the FX3APIguide this means that the FX3 2 stage booter doesn't support switching back. Before calling this function the CyU3PUsbSetBootSwitch(CyTrue) is called.
Thanks for you answer and link. I 'll try this out and report back if I get anywhere. When Cypress included the CyU3PUsbJumpBackToBooter function in the USBBulkSourceSink example I thought it would be as simple as just calling this function. Other people seem to be able to get it to work :