Yes, you can get the data back. Here's what you need to do:
If you have any data in 5.0 that is NOT in version 4.6.8, run 5.0 and export those missing entries in .cdpedia format. Then quit CDpedia and delete the Database.cdpd file from your CDpedia data folder found in your Home folder under ~/Library/Application Support/CDpedia/Database.cdpd. (If you're on Lion, it hides the Library folder by default so to go to your CDpedia data folder you have to use the Finder's 'Go' menu, select 'Go to Folder' and copy paste ~/Library/Application Support/CDpedia into the window that appears.)
Now restart 5.0 and the program will be forced to update the old (4.6.8 ) version of the database file again so all your data will be included. After that's done, you can double-click the .cdpedia export file to import it into 5.0 and you're all set.