[itimpi]

I do not see what you can do to recover the books except see if they are in a trash can, or recover them from your backups.

I am not sure quite how you managed that as there are some checks made that should prevent it happening unless you have done something that manages to circumvent the checks? It is not a consolation, but I would still like to understand exactly what you did so that the checks against such accidents can be improved. Also, what version of Calibre2Opds were you using - some of the checks were only introduced in the 2.4 series. However I suspect you are on the latest so that it sounds as if the existing checks should be improved if the combination of settings you used that triggered the issue can be identifed.

Normally you would set Calibre2Opds to the folder containing the Calibre library, and create the catalog as a sub-folder of that (the catalog HAS to be a sub-folder of the Calibre library folder to operate correctly). Calibre2Opds will have checked that it has a metadata.db file in the library path you specify before it would even start attempting to generate a catalog. It should also give you a warning that the existing contents of the catalog folder would be purged if it did not find an existing calibre2opds catalog at that location.