I had the same exact problem the other day after my wife was d*cking around in my account on our iMac to watch some TV show I downloaded (she didn't think she could watch it from her account). It really pissed me off cuz I have sidebar favorites set up in a very specific way and now they were just...GONE and I couldn't seem to get them to come back, no matter what I tried.
After interrogating her rather harshly, using some expletives and sexually discriminatory remarks about women and computers, I decided I needed to calm down and take a deep breath, during which I restarted the iMac. When the computer came back online, there were my sidebar favorites, magically restored.
May want to try that, if you haven't already.
Don't know how it happened, never saw it happen before and don't know if it had anything to do with my wife's actions, but she claims she didn't do anything - don't they always?