Sometimes (although Apple has largely fixed this of late) when you first turn on FileVault, your whole home directory can appear to have totally disappeared, making you think you lost everything. In every case where this has happened to me, my data was perfectly fine. The problem is that a key setting is not being set correctly -- basically, the setting tells OS X where to find your now-encrypted data.
Go to /Applications/Utilities and open the NetInfo Manager application. Select the users item in the middle column. In the next column to the right, find your username. For this example, I'll say the user's name is foobar. So, find foobar and select it. On the bottom of the window are a set of properties and values for your user account. Scroll through them to find the home_loc property. If this property is either missing or not set correctly, Mac OS won't properly mount your FileVault protected home directory, making it seem like all your data went missing.
To check the setting to make sure it is correct, first click the lock icon in the bottom left hand corner of the window (if it is not already unlocked). Assuming the home_loc property exists, click its value and make sure it is set to:
<home_dir><url>file://localhost/Users/foobar/foobar.sparseimage</url></home_dir>
Where foobar in both cases should be your username. If this is not what it is set to, or if the home_loc property doesn't exist, correct it.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20051203213440779