I'm not sure how this could happen, data files are not removed. What version did you update from? Have you tried restoring a prior backup? Look in the C:\Program Files\Logbook Pro folder (or where you installed the program if different) for a file ending in .OLD and e-mail it to email@example.com. You can also try copying this file to C:\Temp, rename it to end in .BAK then within Logbook Pro restore it (File..Archive..Restore).
Lastly, have you confirmed there is no data such as going to the Analyzer or the Explorer. I just want to make sure it is not a simple layout needing to be restored.