Something like that happened when I was wrestling with learning basic install 101 this weekend.
I copied an index file in WS_ftp over to the server and forgot I had the 'administrator' directory open
and Ka-blooy, instant mess. :-\ Then I deleted the index files because I was going to replace them and
BAM I rememered I did make any copies... (index files from other directories don't work in the administrator director!!!)