I've seen this before, but we couldn't find the cause of the issue, and other forum members didn't seem to be able to re-create the problem. I and two assistants even tried marking down the sync points on the clips, and the marks came apart by themselves.
Try just dragging the synced clips into a bin in the Browser, rather than subclipping.
But next time, don't capture all your takes as one long clip. Bad way to work unless there's no alternative. You save a couple of minutes at the log/capture stage and it can cause you many headaches down the road.
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