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I don't know if it is a problem with ID. However, you can solve it with some careful RegEx. The reason that the links don't work anymore, is probably that the id-names are not unique anymore. All id's in the anchors must be unique.
You have to check each chapter to solve it. I personally would recommend something like: id<chapnr>_<note number>. So, the second note in chapter 3 would be id3_2. That would make it unique. For the backlink you could use idref instead of id.
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