Sounds like there might be room for a complementary function to the Database Integrity check function that looks through all the folders in the calibre library, and if it finds any books there that are not in the database adds them back in (if necessary renaming the folder).
Does anyone see any fundamental issues with such an idea (Kovid in particular), or is someone else already looking at doing this? If not it might be a good excuse for me to start a little programming project along these lines. If I DO start this I would be thinking of also making a change to write the .opf file to a folder whenever the metadata changes as this would be useful in reconstructing entries in the Calibre database, and also means there is a copy of the metadata external to the database itelf if the database ever gets corrupted without the need to do a "Save to Disk" function.
Feedback welcomed on the idea.