UPDATE: In further testing, I did fine the "Video Passthrough" checkbox in the advanced settings for a conversion task, but as soon as I selected the option to "Merge all files", that pasthrough option disappeared (that is why I couldn't find it before - I am testing the Merge function).
I am running another test now, where I checked that Video passthrough for both input files BEFORE selecting the Merge option, but I quickly got a crash report, so I don't expect much from that.