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@gtsueng, it looks like the actual duplicates are stored in the database as you can see from one view but same annotation stored many times... same start, text, view and user. Here is the code I used to check in the shell--I didn't use any code related to the exports. I am directly taking this data from the DB, so unfortunately I think it's related to the db, not the exports.
Based on what I've seen, this bug is still adding duplicate annotations to our db. Fortunately, the duplicate annotations are only 0.12% of anns in the db.
Maybe it's the way the annotations are being queried or merged but it looks like the export files have duplicate annotations.
Example from group 26 in tabular format:

From original xml dump:


In above, the annotation ids appear to change, but it looks to be the same annotation from the same user.
Another example:
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