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Sorry to hear that ezPDF has problems with dealing with columns. I find it has redrawing issues even in single-column text, which is why I am constantly manually refreshing the page. But the inter-operation with Adobe and other PDF readers is one of the main reasons why I stick with it--if I can't use my annotations cross-platform, cross-software, then the annotations are useless to me.
I don't know if there is a setting in NeoPDF to allow for automatic overwriting of the original PDF with the annotated one. I know that ezPDF has that setting. If NeoPDF does not, then I'm afraid that it's unlikely that using a different syncing program will solve your problem.
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