Custom Columns are part of metadata.db
So the Big question:
How did you 'recover'?
If you re-imported (via Add books), you got what you saw (and there is a good chance you stomped upon the files that could have helped
)
metadata_db_prefs_backup (in the root of the library) helps restore the structure <<
metadata.opf
in each book folder helps Populate that structure
Any change to the data or structure causes a background job to keep the metadata.opf current