I'm not sure what your question is. That HP web site you gave a link to refers to "Taking Ownership" of folders and files after experiencing some problems with accounts in XP. I assume that worked for you.
But you mention that many programs were deleted. That would be normal after a system recovery as the Registry is replaced with a new one, and all the programs you installed yourself will have lost their registry entries.
The only way to resolve that is to re-install all those programs/applications. There is no shortcut to this.
I recently did a system recovery on my desktop (HP pavilion 504n - window xp home edition). After the recovery, I manage to get all my files in "My Documents" but many programs were delete. However, my c-drive free space remained the same as before the recovery.
Here is what I did after the recovery. http://h10025.www1.hp.com/ewfrf/wc/document?lc=en&cc=us&docname=nph00268&dlc=en
Thanks in advance.