If you convert a book the data is embeded in the converted book file.
If you have several formats of the same book the formats not converted will still have old info, covers.
The file that is first imported (with automerge checked) will be the metadata that is stored in the database.
If you generally convert to one format, than you should import all of the books with that format first.
Any books not converted after changing metadatstill have old metadata.
If you have .opf files in every folder then you can get the metadata from them by using the second option under add books I believe and this should be the editd metadata.