@drjd
I do not think that you have to do anything. Under the assumption that you lost your annotations caused by one of the possibilities mentioned by Davidfor, all your books on the external sd are already registered in the database, the reading positions and so on however reset to start, and the annotations lost (that means you have exactly the situation that you would get by reformatting and so on).
You can simply start reading your books again and make new annotations. Do not forget to make backups.
@JSWolf
For those who prefer the link to the post providing the annotation extractor rather than the download link:
here it is.