In the past month or so I've noticed a small but noticeable number of users losing their root.disk files (or the entire \ubuntu\disks\ directory). The reason for this is unclear and, so far, the recovery rate is 0%.
In one case, booting from a live CD and running "ls /host/ubuntu/disks gave the following:
# cd /media/win/ubuntu/disks
# ls -l
# d??????? ? ? ? ? ? disks
It's hard to know from the other side of the internet what attempts have been made to recover. But suggestions to run chkdsk don't seem to fix the problem. It's also impossible to know whether this is a new Wubi problem or whether this is a regular issue that has always affected Wubi. Time will tell.
What can you do in this case? The best insurance is a regular backup of your root.disk file, or the important contents contained within.
On that note, I also saw a thread where a user tried to reinstall Wubi to fix a problem. Reinstalling Wubi will always remove the current install, delete the root.disk, and destroy any existing Ubuntu data/settings.
Unfortunately I also see many community members advising Wubi users to uninstall because they assume the problem is Wubi-related. Often this is not the case, but rather it is a normal Ubuntu problem that can be solved (and would still have to be solved after replacing Wubi with a normal install). It is important to let these well-meaning members know that this advice could destroy the user's important data. It's not hard to add a cautionary warning, and perhaps suggest to the user how to recover data from a root.disk from Windows (e.g. http://ext2read.blogspot.com/) before uninstalling.
A final comment... in my opinion, reinstalling an OS is not a solution to a problem - it's the last resort when there is no solution. All too often I see users quickly reinstalling at the first sign of a problem e.g. when their master boot record MBR is overwritten by Grub2. This is the simplest thing to fix and doesn't damage installed OS's or their data, so if they could just resist the urge to give up and reinstall it would save them a lot of trouble.
And remember - you can rid yourself of Wubi, but not lose any of the look and feel, settings or data on your current Wubi install, simply by migrating. There is a new migration script coming soon that supports grub-legacy (Wubi installed prior to release 9.10 and later upgraded) as well as migrations from a live CD/USB simply by pointing at a root.disk file.