When you open the file in your Reader Library, you should be able to view your annotations. From there, you should also be able to export those annotations to an RTF file.
But you mention that when you open the file in the Reader software, your markups are not there. I never really had that problem. Are you sure you are opening the right file? For example, if you upload the file to your reader software, then transfer the file to your device, then annotate the file on your device - of course the original file, on your desktop, will not be annotated. But the file on your device should be - you should be able to open it in the reader, transfer it over to your desktop and export it to RTF, if you so desire.
Are you sure you are not simply looking at the original version, rather than the annotated one?
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