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Here's what I do to create mixdowns and stems. I don't know if my process is a work-around or whatever but it's what I've settled on. Before I begin, it's important for me to mention that I do NOT run my instrument plugins from within Qtractor itself. Instead, I run them in Carla which I send to over MIDI busses. The audio is then sent back to audio busses I maintain in Qtractor. Essentially, I use Qtractor as a router of sorts. Effects are handled much in the same way 99% of the time although they make use of Aux Sends which send to their own dedicated audio busses. I'll assume this basic mode of operation is understood and move on to the setup I use to create a mixdown (all tracks) or a stem (individual track either wet or dry depending on the on/off state of the plugin sitting in the bus).

Mixdown or Stem recording process:
1. Add a new audio track named "Mixdown". Input is "Master" and Output is "Mixdown". Bring Gain fader to 0 (or -70db) <- VERY IMPORTANT!
2. Enable Record on "Mixdown" track, Record then Play in transport (in other words, the usual recording process).

When all tracks are unmuted, we are mixing down the entire track. Likewise, I solo a particular track when I'm rendering a stem. The process can be extremely time consuming but I'm fine with it. The only side effect I've noticed is that my stems can be a tad longer then the original material and not quite line up with the MIDI. I've learned to evaluate this on a case by case basis and adjust the stems as needed. From past conversations, I'm confident this is a result of the "loopback" nature of my setup/process. Fine, I've learned to live with it. :)

Hopefully this has helped. Feel free to let me know if something is unclear.