I have this exact same issue. I have created a macro to do an 'Over-The-Air' (OTA) update for a Teensy microcontroller. The macro works fine starting with no Tera Term connection, but fails if a Tera Term connection already exists. Since the Tera Term connection is how I get status updates from the Teensy, it is always open - so I have to close it before starting the update process.
I tried using the 'testlink' command, but this doesn't find an existing Tera Term window, so is useless for this purpose.