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We've all had the experience where Premiere couldn't auto-sync audio and video, and so we switch the timeline to Audio Time Units and get to nudging. (I've also recently learned that you can use a multi-camera source sequence to auto-sync and merge audio and video). That is only where my problem begins.
Once the video and audio are "linked" together, either through merging it myself or via multicam or nesting, THE AUDIO IS NO LONGER ALIGNED! This is after Premiere supposedly aligns the audio by its exact waveform, or I do it manually by eye.
I've tried switching the timeline back to frame count after aligning via ATUs, trimming the video and audio, and then merging, and it still happens.
Here's an example of auto-synced multi-cam on my timeline. This is a clap, and the de-sync creates a very audible clap-clap.
Here's an example of a manually synced & merged clip, placed back into the timeline: 
Again, the clap very distinctly sounds like a clap and a half because of the de-sync.
hardware / software specs:
I really don't know what to do about this. I've been having this issue with Premiere for 10+ years and a fix has never been made for it. It's like the program is overriding where I place the audio on the timeline. Please help.
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Wow, that's a total bummer. But also quite puzzling ... I've been using Pr for over a decade, with a ton of both Multicam and manual syncing, and never had this happen.
So I'm totally puzzled ... the only differences I see is that you're on Mac, and the sequence was vertical. Which shouldn't cause a problem one would think. Huh.
@PaulMurphy ... any help you could offer?
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The way Audio Time Units work in Premiere Pro can be a bit unintuitive. When you nudge an audio clip using Audio Time Units (ATUs), its position is maintained with sample-level precision—but only until the clip is moved or edited as part of a video selection. Once that happens, even using Edit > Undo won’t restore its previous ATU-aligned position.
This behavior is one of several reasons why merged clips are not recommended. They can often introduce sync inconsistencies, especially when precision is critical.
For a more reliable workflow, I recommend the following:
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