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Do you have any odd mute keyframes on any of the tracks?
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Not so much keyframes that are muted but whole clips. But it appears to be random clips that are muted on export in each track.
I've also been talking through the problem a bit in reddit for more context:
Still no luck though besides manually transcoding each not working clip into an aiff which is a long and tedious process Id prefer to avoid
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Hey, I'm feeling your pain. I just made a new draft of a music video I had been working on - 2 tracks of audio that exported just fine for the first 4 versions. Version 5, literally a copy of the previous versions as far as audio is concerned, same settings, etc.
While I have no solution, I can tell you that after tinkering with settings, emptying cache, making sure no tracks were muted, etc, I tried exporting via Premiere rather than ME, and that worked.
Not an actual solution, but might be a band-aid.
Hope it helps!
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Also, for the sake of completeness, I'm working with
Catalina OS 10.15.7
3.2 GHz 16-Core Intel Xeon W
128 GB 2933 MHz DDR4
AMD Radeon Pro Vega II Duo 32 GB
Premiere Pro v14.7