I think what you did was right. From what Davidfor related on another post I was expecting it to work.
If copying the Digital Editions folder does not bring back the annotations and you need them urgently, you can try something. You could copy the KoboReader.sqlite that you saved before resetting the device back to the device now. This might, however, involve some dangers. If your ADE problems were related to the database, you will introduce them anew. Therefore, I would rather copy the bookmark entries from the old database to the new. In order to avoid interfering with the bookmarks of kepubs, which are handled by the synchronization, I would copy only those bookmarks of which the ContentID starts with "file:///mnt/onboard/". If you do not know how to do this somebody on this forum can certainly recommend which tool to use on your OS and provide you with the right commands. In any case, save your current KoboReader.sqlite again for further use in case something goes wrong.