That's a puzzle, as MixPres don't actually make stereo files, although it may seem like it in some circumstances. They make one polywav file for each recording, with as many channels in it as you have selected to record. Yes, you can also record your stereo mix along with the ISOs.
How did you determine that you have a 1-2 stereo track when recording 2+ ISOs?
I have access to the MixPre10 and 10ii (no Musician plugins), but I believe they work the same as the 6. The polywav is not well explained in the manual. The recorded polywav file will have as many tracks as you have recorded. If you only record ISOs 1 & 2, you get a 2 track file, which plays like most stereo WAV files. If you record ISOs 1-2-3-4, you get a 4 track polywav. Ensure that your playback knows what to do, and doesn't just play the first 2 tracks assuming it to be a 2 track stereo WAV. Likewise for your playback computer, most will probably only play 2 tracks of a wav file.
Note that you can enable/disable recording the stereo L/R mix in the menus (RECORD/RECORD L,R). When enabled, the MixPre always makes this the first 2 tracks of the polywav. The armed ISOs then fall in place in order. If you record the L/R mix and ISOs 1-2-4, you get a 5 track polywav with L,R,1,2,4. It won't "skip" and record a blank ISO-3 if 3 was disarmed. If you record ISOs 1-2, you get a 2 track polywav that seems like stereo, but isn't really designated as such.
Sound Devices provided the Wave Agent app to help split out the polywavs into separate tracks, but it won't work on 32b float. Apps like Reaper can take the polywav and show all of the tracks in it, and let you split the tracks out for full remixing.
I’m experiencing some unexpected behavior with my MixPre6. It’s probably my fault but I can’t make sense of it -
When I have two or more ISOs connected, ISO 1 and 2 always save as a stereo track, and I’ve triple checked that these channels are not linked. It’s making me paranoid that it’s a stereo mix down of all the connected ISOs (it’s not but I’m still paranoid about it). I would feel much more comfortable if these would save down as discrete tracks, but other than unlinking channels 1 and 2 there doesn’t seem to be much I can do about it.
Followup question - is it possible to save a stereo mix down in addition to the discrete ISO lines? That seems like something many would want to do, even though I don’t want to use it that way. I struggle to find anything in the settings that suggests I can.