danicca: The main way you could cause the database corruption is by not safely ejecting the ereader from the PC before disconnecting it. As the device ran out of space, the corruption is probably related to that. I suspect that the loss of bookmarks are related to this as well.
Doing a logout will remove the ADE authorisation. But, you can get ADE to do this again on the next connect. But, you can also take a copy of some files before the logout and restore them. Take a copy of all the ".adobe-digital-editions" directory. After logging out and back in, restore the directory and all the files in it. At least one of the files is hidden, so make sure you have both the "device.xml" and "activation.xml" files.
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