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Trouble sending serial UART message with flow control enabled

I'm developing on an nRF52832 that has a serial connection with an iMX6 that is running a Python script with pySerial. For a while I had flow control disabled and would get frequent overrun errors. After enabling flow control, I must reset my Python script in order to have valid communication. Specifically, the Python script does not register that a message was sent and the irq_handler is not triggered to register a NRF_UARTE_EVENT_ENDTX. After the Python script is restarted, the nRF52832 has a NRF_UARTE_EVENT_ENDTX event and the iMX6 receives the message. Why is this happening? What can I change so that I don't have to manually restart my script?

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