Timecode synced audio clips become unlinked at random and are impossible to export

Using the latest version of Premiere (15.1.0) in MacOS Mojave, I started a new project and synced up a video clips (with in-camera scratch track) to three lavs (recorded independently to a mixer) with the timecode generated by my Tentacle Sync. No problems there. But when I made an edit and exported a ProRes422 file with four audio tracks, I noticed that the lav tracks had stretches where they were silent. When I went back into my Premiere project, I noticed that some of these lavalier audio tracks were showing the diagonal lines:



I hadn't changed any file names or moved anything, and I'm not seeing any indication of broken or missing links in the Project panel. But I cannot hear these diagonal "unlinked" tracks when I solo them in the timeline. However, I can hear them when I double click on them and bring the waveforms up in the Source panel. Just to rule it out, I've tried relinking them in every way I could think of, but that didn't make a difference either. And of course, I tried rebooting. No luck. I even started a new sequence and reconstructed the edit. The diagonals issue didn't show up right away, but it did eventually happen.

What really baffles me is that it's not ALL of my lavalier recordings. Just some of them. And a few of the clips are partially in diagonals:



The non-diagonal portion plays back fine on the timeline.

Anyone know what's going on?
 
They are all 24 bit, 48000 Hz.

What's really crazy is that in several cases, the exact same wav file is referenced by both working clips and problem clips.
 
I would suggest trying to clear cache and then importing the project to a completely new project. Clear all cache, create new project, import your old project that's got the audio sync issue into the fresh project. This method has worked for me with a lot of similar issues.
 
Maybe try transcoding the original audio files (just 2-3 for a test) into another format and importing them again into the project and swapping them.

Although rarely, sometimes - for what seems like no reason at all - files get corrupted during the editing process (even if they appear fine).
 
Good idea. I converted all of the WAV files to AIFF and relinked, but the issue persists.

What I'm seeing now is that the non-diagonal areas are out of sync. And the diagonal areas aren't having trouble linking to the files, they are linking to a timecode that is before the beginning of the recording. Somehow the timecode has slipped in several places. I have no idea how. If I had the patience to do it, I could use the slip tool to move correct each of the hundreds of clips.

My scorched earth solution: export a multi-track MOV of the original synced up sequence, video blackouts and all. Then I'll cut that down.
 
Try other software if possible.

If you can cleanly import all of your footage with all of the audio correctly synced (some parts may require duplicate versions depending on the audio/speaking), maybe you can export high-quality masters of that and edit that. Although depends on how far you're in post.
 
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