Strange problem with audio sync

I work at a university helping students with any problems they might face with video editing and post-production. Recently, a couple of students asked for help with a problem they were having with the audio sync.

They recorded video with a Canon 5D MarkIII and the audio with a separate device (I'm not sure, but I think it was a Sound Device, but I can't remember the model). Then, they put all the clips in a timeline (after converting the video to Apple ProRes 422) and synced the audio, maintaing the original form the camera as a reference. After that, they linked the clips with the synced audio and dragged one by one to the bin, forming a new clip. When I double-clicked the clips, they were just fine, the audio was correctly synced e working. The problem appeared when they created a new sequence with the same settings of those clips. Suddenly, all of them, in the new sequence, were out of sync and we couldn't sync it again (though the original sequence where they did it manually was still ok), not even after changing the speed and duration. We verified the clips and they were just the way they should be, with the very same settings they had in the other sequence. As an alternative attempt, we created another sequence with the same settings. Inexplicably, it was all normal.

Though somehow we managed to solve the problem, the first sequence where the synced clips were imported remained out of sync no matter what. I don't know why it happened and everybody I know with experience in FCP couldn't help because they have never seen something like that. Does anyone know what could it be?

Best regards

Audio sample rates are not matching somewhere. Or this is typical of that issue.

If the sync works fine in the Browser copy, export that as a baked-in QT file. Re-import and be done with it.