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pleiadesc - see ==>>
Annotating PDFs in OS X w/o modifying the file. This utilises a pdf reader/annotator called SKIM which saves annotations in a sidecar file (.SKIM), but SKIM is only available for OS X.
I'm not aware of anything similar for Linux or Windows, but there are many pdf reader/annotators, especially for Windows, maybe one of them can save the annotations in sidecar files like SKIM.
How do other Zotero users handle this, did you ask in the Zotero forums?
BR