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Sounds like the problem is actually with the way the Dropbox app works? Have you tried using Dropsync instead? That works in the same way as the Dropbox desktop client: you identify entire directories to always keep in sync. You'll end up with duplicate copies of the papers you've annotated, of course, but no system is perfect.
[I much prefer ezpdf because annotations are interoperable with Adobe, Okular etc, but I don't have to deal with columns so often.]
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