When it finds an item that matches it is to copy this item to the corresponding folder (the folder who's name matches the first 4 character of the file name).

Sounds like your desired folder is a subfolder of $to_dir. Instead of

        copy($i,$to_dir);
[download]

assign that four-character string to a variable so you can

1. check for the existence of a subfolder with that name, and
2. copy the file to that subfolder.

The capture variable $1 holds the string you want if the match succeeded, otherwise it may hold something left over from an earlier successful match. So don't use $1. Say

FILE:
for my $file (@update) {
    my $first_4_chars = substr($file, 0, 4);
    next FILE if not $seen{$first_4_chars};

    copy($file, "$to_dir/$first_4_chars");
}
[download]

Oh, and please

use strict;
use warnings;
[download]