Premiere workflow: Maintain multichannel sync from dailies through edit lock to sound?
The Subsequence Method:

This is the first method I developed to work in this situation.  I'm posting it as an answer here because it might be a sufficient answer for someone with a similar problem.  However, I do not consider it a good or elegant solution.  It has serious drawbacks which complicate the editing process (Subsequences don't display audio waveforms on the timeline, using Shift+O to open in source monitor is awkward, e.g.). I mention Reaper in this answer because it's the specific DAW we're targeting, but the advice might be generalized to other DAWs. Vordio is a translation tool which works in this context, but I cannot comment on its efficacy in others; YMMV 


Select all of the Zoom audio, right-click on it, and “select modify audio channels.” Change number of audio clips to 1, set clip channel format to adaptive, click OK.
Create a new sequence from the file menu, making sure that the audio tracks are adaptive.  This first sequence is just for sync dailies, so you only need one adaptive (or stereo) track on A1 for camera scratch, and a Poly on A2 for Zoom audio (with # of channels depending on how many sources used by the recordist.
String out the video by selecting it all, and clicking the automate to sequence button.  The camera scratch audio should land on A1 when you do this.
Drop Zoom audio on A2 and sync each clip, one-by-one, either by using the “syncronize” command, or by lining up slates
Once you’re done syncronizing, delete A1 camera scratch.  You don’t need it any more.
Select each A/V clip pair in turn and “Link”.  This step’s kinda optional, but without it, the Subsequences generated in the next step won’t be linked.
Select each linked pair in turn and “Make Subsequence”
Re-name all of the subsequences.
Now, make a new timeline for editing.  Since double clicking subsequences in the project browser doesn’t open them in the source viewer like regular clips, you’ll want to use Shift+O (That’s an Oh, not a zero) instead.


Edit your material

Once your edit is locked, you need to flatten the subsequences before sending to reaper.  Follow these steps.
Basically, make sure the “insert and overwrite nested sequences as nests or individual clips button” is disabled (white, not blue)
Make sure selection follows playhead is enabled
Lock any tracks you don’t want to affect, and make sure the sequence targeting is active for the track you do want to affect
Repeat the keyboard sequence: [ x ] [ f ] [ . ] [ shift+3 ] (ex, eff, period, shift key and number three together) for every clip in the timeline.

Now, to export a project for mixing, follow these steps:


Command+M
Set Format to Quicktime, Chose Apple Prores Proxy from the Preset dropdown. Under the “Basic Video Settings” section of the “Video” tab, uncheck the box next to width and height and change either number to a quarter of their original size.  The other number should scale by the same amount automatically.  If it doesn’t, make sure the link icon is active.
Under the “Audio Channel Configuration” section of the “Audio” Tab, change “Output Channels” to match the number of channels in the poly wave.  Make sure all of the other, “Basic Audio Settings” match the quality of audio the recordist started with.
Hit Queue, and let Media Encoder do its thing.
Now, to translate via Vordio for Reaper, follow these steps:


In Premiere, do File->Export->Final Cut Pro XML.  Use the default Final Cut XML version.

Download Vordio if you don’t already have it (http://vordio.net/download/) , and open it.  In the “Convert Project” tab, click “Browse” by the “Source File” field, and navigate to wherever you saved the XML.   Browse for an Output Folder the same way, and click convert (all of the other settings can be left at default)