where are the files

the may have to be answered in the apache httpd forum but I thought I give this a go first.
had a directory scripts.
it was aliased in the apache config.
Here is the linux part
all the files have disappeared from the folder but I can see the files being included in the webpages.

so can the files be moved somewhere and redirected some how, like you do with other linux files.
if so where should I look for such information.

my concern now is that someone has access to my server and is playing games.

You can use
Option FollowSymLinks
in directory container in configuration file, to redirect the files.

Thanks but that is not what I was trying to find out.
Actaully I found the files by going into the server through VNC.
they don't show up under webmin so I have gone to thier forum to find out what might have caused thier file manager to not show the files.