We've never encountered that, but if the VM was powered down while UR was updating the database, it is possible for that sort of thing to occur (probably more likely on a shared vs local file). See here for how to minimize when UR updates the database:
http://www.kinook.com/Forum/showthread.php?t=3728
This could slow UR down, but you could also set the SQLite synchronous level to Full (default is Normal) using the attached .reg file. See here for more details:
http://www.sqlite.org/pragma.html#pragma_synchronous
See here for possible recovery options:
http://www.kinook.com/Forum/showthread.php?t=2673
And of course, we recommend that you always keep a regular backup of important files.