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The intent is to merge already-stored annotations with new annotations. Merging is done in annotations:merge_annotations() around line #229. Replication of existing annotations is avoided by comparing hashes. I'm not sure what would cause the behavior you're describing.
I am traveling with infrequent internet access until early January. When I get a chance, I will do some testing to see if I can replicate the behavior you're describing. In the meantime, if you identify an issue with the current code, please create a new issue at GitHub.
G
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