We have never heard of something similar. Could you please send us more information about what exact errors you're getting as well as your console log. You can access the console log via the application 'Console', located inside your Applications/Utilities. The newer messages are towards the end of the log. You can search the log and gather the entries from DVDpedia and Bookpedia. It would be very strange for both to start acting up at the same time.
The covers are located in the respective data folders, inside a folder called "Covers". Can you verify that the covers are still there please? DVDpedia would not delete them, so it must be some other kind of display bug that is affecting your computer.
Actually please email us your data file so that we can better help you as well with specific information about which exact covers are missing. You will find the database in your data folder located in your home folder at ~/Library/Application Support/Bookpedia/Database.bookpd. Under Lion you must use the Finder menu "Go -> Go To..." command and enter "~/Library/Application Support/Bookpedia" to open the folder. Once there select the Database.bookpd and use the "Compress" command under the main "File" menu. This will create a .zip version that you can then attach to an email message.
From there I'll have more details and we can try to find out what is going on. Do not sync with Pocketpedia in the meantime to avoid any issues.