Those OPF ARE what the RESTORE uses to rebuild the DB .
This is a different (and way faster) process that doing an ADD, since the metadata was known.
If they were missing BEFORE the restore, then the DB never built them (this is a background task that chugs along at a OPF every few seconds, when needed.
Library Maintenance: Library Backup Status. It will be drop to 0 when caught up after a large amount of changes) . You may have shut calibre down one last time, before your system had time to catch up)
Or the DB had accumulated those errors to begin with.
Now, the recovery invokes Identifying the Unknowns: Dragging them OUT of the Library FOLDER: The Add those normally