The 1000 Genomes FTP site under goes periodic rearranges to accomodate new data sets coming in
and preserve old data in a new location.

If you have a particular file that you don't know if it still exists the best place to try is
our current.tree file

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree

This file contains 6 columns

Relative path
type (directory or file)
size in bytes
last updated time stamp
md5

You should be able to search this file with your filename and see if the file still exists and find its new location

If you still can't find your file email info@1000genomes.org and the support team will be able to tell you what has
happened to it.