Well, I came up with a solution. It isn’t the most elegant…
For this to work, I have to preserve 1 source level in Resolve, Which I do anyway. It also requires FFMPEG. I use the latest one from macports. (sudo port install ffmpeg-devel)

In my folder naming, I put all my Original footage in a folder called Original, then I have a folder for the Editor, and another for Dailies… So I made a script that will use FFMPEG to copy all the video and audio to a new quicktime, then replace the source quicktime it used if it was successful.
here is the script:
#!/bin/sh
if echo "$@" | grep -q Original ; then
echo "This is the Source media. Please use the proccessed media..."
exit 1
fi
for h in "$@"; do
if [ -d "$h" ]; then
for i in "$h"/*.mov; do
ffmpeg -i "$i" -map 0 -map -0:d -c copy -channel_layout mono -movflags +faststart "${i%.*}---.mov" && mv "$i" "${i%.*}-org.mov" && mv "${i%.*}---.mov" "$i" && rm "${i%.*}-org.mov"
done
fi
i="$h"
if [ "$i" = "${i%.*}.mov" ]; then
ffmpeg -i "$i" -map 0 -map -0:d -c copy -channel_layout mono -movflags +faststart "${i%.*}---.mov" && mv "$i" "${i%.*}-org.mov" && mv "${i%.*}---.mov" "$i" && rm "${i%.*}-org.mov"
else
echo "$i is not a Quicktime file. Skipping."
fi
done
If you done want it to delete the source file, then remove && rm “${i%.*}-org.mov”
I saved it to ~/bin/fixaud. Then did a chmod +x ~/bin/fixaud.
So all I do is open a terminal, type ~/bin/fixaud then I drag the folders I want it to fix the audio on, and press return.
The bad part is that the Reelname gets stripped.. For that I use a program called QT Change. It is $25, but has a demo that you can do 8 files at a time. It is well worth the $25 to have it add the reel names based on the folder it is in for all the files.

I guess this will be my workflow, unless someone can come up with something better…
— Benjamin