I'm not sure about annotations being corrupted, I only ever made them on a temporary basis, usually proof-reading my own work. But I do know that since DR800+ they don't work any more.
This may be the wrong thread, but I know you are the author anyway, so can I report another problem. I installed FBReader 2.10 v3b to see if it would make a difference. It actually made my DR800 behave very strangely - if I suspended it with PDFs open, the light would continue flashing. Also the time it takes to load a PDF page was greatly increased compared with the last version of the DR800 software (was that called version 2?). So I tried to uninstall, but that made no difference. It looks to me like the uninstall failed but I'm not really sure how to check what's going on.
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