Let's regress a bit. Based on your responses, we know you are an
experienced user. So, lets try to think of ways that files can be
deleted or hidden.
Is it possible that something might have changed the partition table,
so now you are mounting the wrong partitions. I've done that to myself
a number of times without thinking.
One of the best ways to track this down is:
1. Boot to single user with only root mounted.
2. foreach partition (use fdisk to list your partitions on all your
drives).
mount partition on /mnt
cd /mnt
find . -name <a missing file>
cd
umount /mnt
This can be tedious, but it is one way to find out if your files are
still there. Make sure the file you are looking for was definitely
there previously. Also, by using this method, you can assure yourself
that you did not inadvertently mount another file system over a
directory.
Just one more question, did fsck report any errors, either before you
lost your files or after you lost them.
--
Jerry Feldman