I don't have a clue about using DFF files .. but if they are like ISO files they may be considered as data files not audio. Whether or not tags are saved to sidecar files or not, I'm not sure. I do not believe you can write tags to this type of container, but frankly I'm not sure either
Be that as it may, if some dff specialist does not chime in. I would run an autoimport as your configuration and undocking the drives could break the links. You could check this by creating a smartlist for this =>
http://wiki.jriver.com/index.php/Broken_LinksFirst to confirm, you are saying that the files exist in the library, but the player can't find them right? Not that they have disappeared from the library completely right?
If so, I would manually back-up your library and save a second copy of it (MC does this automatically, but not necessarily when you want/need it to be done. look int the individual folders containing these files. If they have xml or other sidecar files, back these up.
Then I would change you import settings to include the drives with fix broken links, protect missing drives and the external change option checked. Manually run auto-import. Does this sort everything for you? If so, the undocking probably has broken the links. If all your data has disappeared for some reason (like dff files have some different way of handling the metadata that I'm not aware). No worries just restore your library backup file. There is an option to NOT automatically import files. Autoimport is sort of a misnomer in my opinion. However you still need to configure the import options (see the wiki articles for Import and Auto-import on this Robert).
You could also try to update tags from library to see how/what dff filetypes actually write to disk. (Right click on file=>Library Tools=>Update Tags from Library. Warning: as I said, I don't know where the tag info is stored for DFF files (library only, partially in container, sidecar files?)
as I said I'm no expert on DFF files so make sure you have everything backed up! before messing around. If all the links are borken you might have to re-point the database to include them.
Question, why do you not have any folders selected for import? Personally I prefer to have the broken links option selected .. there might be reasons you don't want this? Are the missing files all located on the same drive or parent filepath?