Wouldn't a button within the RTTViewer that resets the micro make sense? Then the RTT viewer could perhaps handle or ignore any buffer corruption issues.
Currently pressing the hardware button and I assume resetting from the micro itself or pin would work usually. I don't want to use the down buffer to tell the micro to reset as that would cause power usage etc. and so I have not implemented it. When I try to run JLinkExe to halt and go then RTTViewer seems to lose it's connection as soon as JLink commander is told to connect.