Here’s my go-to proxy solution. I’ve done some tinkering to my workflow to make this function.
Instead of using Media Encoder for Proxy generation, download a free version of Da Vinci Resolve.
Load all of your media in. Select all your files.
Click File menu > Media Management,
Select TRANSCODE: Here you can batch transcode media.
(Pick a new destination so it won’t amend the filenames of your Proxies.)
Here’s the important part: Under AUDIO:
–Render “SAME AS SOURCE” Channels of Audio
This will generate proxies with your desired codec, but if your channels vary camera to camera, scene to scene, day to day etc, it should reflect those changes.