First, if you haven’t already please update to the latest version of the BBManager: http://mybeatbuddy.com/forum/index.php?threads/beatbuddy-manager-software-1-64-win-mac.6232/
Are the songs just gone on the SD card, or also in the BBManager? Do any of them contain periods, apostrophes, commas, etc? If so, take them out and see if they continue to disappear.
If the issue doesn’t seem to solve itself, please tag me by clicking the ‘reply’ button which will automatically send me a notification that you replied.