Vista ran check disk, "Replacing invalid ID with default S..

Had to switch off my laptop after a bad program hang, and eventually, when
it restarted, chkdsk ran automatically.

it then started pumping out hundreds of thousands (350000 or so) of the
lines
replacing invalid ID with default Security ID for file NNNNN

Luckily, things are not too trashed and I can still read my files after
manually changing them, and I've done a recent backup, but my question is,
how can I best restore the file permissions on my disk to what they were
before. Will a system restore do it?

Or can I use the backup I did a week or two ago, to go back to that point?
It was a vista backup (but because the files are in .zip format, I'm not
sure if it was just files, or if it was a full one).

Any suggestions?

Tony