You are opening two files using the same file handle; so, the second open() closes previously open file. In addition, you are wiping out the contents of file referenced by $destination.

Don't write your own code for copying files unless you have to.
Use File::Copy instead. strftime() from POSIX will help you format date strings.

use strict;
use File::Copy;
use POSIX;

my @files = ('system.csv', 'sales.csv'); # your files
my $home = 'd:/EOD/20 January 2002/';    # source
my $archive = 'c:/New EOD/';             # destination

# the day before
my $yesterday = strftime("%Y%m%d", localtime(time - 24*60*60));

# copy all files from $home to $archive;
# prepend yesterday's date to all file names.
for (@files){
  copy $home.$_, "$archive${yesterday}_$_"
    or print "ERROR: Can't copy $_ : $!\n";
}
[download]

--perlplexer