I also agree with Joebert and Jopoy. The most invasive part in the upgrade path is the change of kernel version which means that you will have new kernel drivers and new scripts for auto-detection of the modules corresponding to your hardware. If the necessary modules for file-system support is incomplete (raid support, lvm support), the new system may still be able to mount your filesystem but will not show the files.... and it is a bad idea to immediately use fsck. if the necessary logical view of your filesystem is not there because the driver was not loaded, the logical view of fsck will be different from the logical view of your actual file-system. its changes will be destructive because it has a wrong view and will try to correct the system. i think there was no problem in your files prior to FSCK.
here's a link from debian regarding upgrade: http://www.debian.org/releases/lenny/i386/release-notes/ch-upgrading.html
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