I'm assuming you have a Windows Bootcamp installation.
The lost Windows data has to do with GPT and MBR being out of sync, but your Bootcamp partition is still there and so is your data. Have you tried booting directly into bootcamp? If that doesn't work there are still ways to recover data from the 'lost' partition if you don't delete it/format those 40GB, this is not directly related to Parallels, but to the upgrade to ML (it could still happen with Parallels v8).
Last edited: Oct 26, 2012