Cross linked files occur when you shut down Windows abnormally
(such as through crashing the OS). Any open files (such as the swapfile
or the registry) would remain opened, and can cause corruption to the
file, cross-links with other files, etc.

They are generally harmless, though. Cross-links are simply FAT
entries that point to the same cluster, but scandisk can normally
sort them out for you. The CHK files it creates are generally useless,
but if you find you've lost an important file you were working on, the
CHK may contain enough data to recover. However, if the file was
anything but plain-text, this task would be nigh on impossible for the
average user. Personally, I don't even create them any more, as all my
important data is regularly backed up in rotation.

The drive is safe to use after scandisk has repaired it. For this reason
alone, it is best to repair the disk after a crash or abnormal shutdown.
Usually, the swapfile will be damaged, but this is rebuilt when Windows
reloads so even if scandisk trashes it, no harm will come. If the registry
becomes trashed, Windows will prompt to restore from the automatic
daily backups. Any other trashed files should be restored by re-installing
the application. If Windows files are corrupt, use SFC to restore them,
or use the DOS EXTRACT/? command if unable to launch Windows.

As always, backups are essential to avoid any disasters. They do happen,
and usually when you least expect it, however 99% of the time, scandisk
will sort you out.

--
    Peter C. Forrest Domain: http://www.pcforrest.co.uk
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    E-mail: pcf at freecall dash uk dot co dot uk