I'm not really familiar with this XDS100 emulator - mostly using other Cortex M boards like the TM4C launchpad and competitor products. But it sounds like you are using a VCP (virtual COM port) provided by this debug adapter. You might need to check if it actually supports hardware flow control. I know of others (on different evaluation boards) who do not - the RTS/CTS lines from the MCU's UART to the JTAG/VCP adapter are already missing.
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