When you run the FPGA VI with an FPGA target emulator, LabVIEW clears FIFOs when the VI stops and then starts again. When you run the FPGA VI on an FPGA target using Interactive Front Panel Communication, LabVIEW does not clear FIFOs when the FPGA VI stops and then starts again. To clear target-scoped or VI-scoped FIFOs on the FPGA, use the FIFO Clear function. You also can right-click the VI in the Project Explorer window and select Download from the shortcut menu to clear FIFOs.
When you control an FPGA VI using Programmatic FPGA Interface Communication, use the Stop method on the Invoke Method function to clear DMA FIFOs from the host VI. Also, the Reset method on the Invoke Method function and the Close FPGA VI Reference function with the Close and Reset shortcut menu option selected clear FIFOs. In addition to clearing FIFOs, the Reset method and Close and Reset option complete other tasks. Refer to the Invoke Method and Close FPGA VI Reference topics for more information.