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I'm in the same boat and have been for the past four years.
I have given up.
IMHO, for me, none of the eBook reader devices (ePaper or similar) offer easy and trusted workflow of PDF annotations, highlights and syncing them properly. Most are kludgy, proprietary and unreliable.
The easiest and most expensive way is just to get an iPad and buy a proper PDF management, marking, indexing and searching app like Papers.
A similar one for Android seems to be Mantano eBook reader, althought not anywhere near as comprehensive.
YMMV, of course.
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