WHS automatically distributes files over drives. You can read a white paper about how it works here: http://www.microsoft.com/downloads/en/details.aspx?FamilyID=40c6c9cc-b85f-45fe-8c5c-f103c894a5e2&DisplayLang=en
If you look on the primary disk, it will have a data partition that appears to have all directories and files. However, some of those files are NTFS "Reparse Points", which just point to a file elsewhere. Through most APIs, attempting to read from a reparse point will return the contents of the the pointed-to file.
WHS Drive Extender has several rules it follows to decide whether to keep the actual file on the primary disk, or just to keep a reparse point there. The rules depend on the number of disks, whether duplication is enabled for the share containing that file, and how full each disk is.
You didn't say how many disks you had or how your shares were configured, but my psychic powers tell me that you have more than one physical disk in your WHS. If you plug the other drives in to your Windows 7 PC and dig around, you should be able to find more of your files.