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I agree. I often read batches of academic journal articles and retrieving them back into Zotero one at a time is time consuming. I've thought about batch processing the files and somehow changing their names but haven't figured out exactly how that could work. It would be easier to automate a batch processing if each annotated file just had _merge after it instead of the time and date.
An alternative is exporting the annotations to a text file and just dragging and dropping that into the zotero items. Again, a far from satisfactory solution.
Sorry, wish I could help you more!
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