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You will find most of the data under C:\Users\<username>\Documents\My Digital Editions
If you back that up (and its subdirectories) and restore it to the new Windows installation, you should get everything back as it was before.
The annotations are under C:\Users\<username>\Documents\My Digital Editions\Annotations
If at all possible, backup your entire drive before reformat/reinstall;
there may well be other things you wished you had backed up and don't think of till too late.
Thanks for helping, but I hope Adobe finds a better solution for this situation. There should be an option to store highlights and annotations and export or backup them up.
I agree it would be good to have cloud managment and storage of the books etc you use under ADE, but I doubt Adobe will provide it.
Unfortunately, Adobe only provides very limited support for ADE and ADE related infrastructure: I suspect just enough to be able to get money from vendors for use of Adobe DRM. No online management of authorized devices, no proper product test (as shown by the huge number of bugs in ADE2.0), ....
If you are a bit technical and willing to play around a little, you could probably get the effect you want.
Use some cloud sync mechanism that allows you to specify your own folders.
Or, use something like Dropbox, and use a directory junction or symbolic link to make the Digital Editions directory part of your Dropbox.
OK, it's a hack, but as I say, you'll probably never get it if you wait for Adobe.
Thanks, sjpt, that's exactly what I'm going to do. The cloud solution seems to be the only efficient workaround.