Do the files exist in the given paths on the machine running the code? If so, you can validate each "edit".

I'd alter the regex creation slightly:

use strict;
use warnings;

my $paths = <<PATHS;
/unix/path/to/folder/is/here
/unix/path/to/folder/is/somewhere
/unix/path/to/folder/is/herewith
PATHS

open my $file_paths, '<', \$paths;

my $references = join '|', map {chomp; qr/\Q$_\E/}
    sort {length($b) <=> length($a)}
    <$file_paths>;

print join "\n", split ('\|', $references), '';

for my $test (
    "/unix/path/to/folder/is/herewitha_file.txt",
    "/unix/path/to/folder/is/herea_file.txt"
    ) {
    $test =~ /($references)/;
    print "$1\n";
}
[download]

Prints:

(?^:\/unix\/path\/to\/folder\/is\/somewhere)
(?^:\/unix\/path\/to\/folder\/is\/herewith)
(?^:\/unix\/path\/to\/folder\/is\/here)
/unix/path/to/folder/is/herewith
/unix/path/to/folder/is/here
[download]

which ensures longer matches are made first. In the example code commenting out the sort results in:

(?^:\/unix\/path\/to\/folder\/is\/here)
(?^:\/unix\/path\/to\/folder\/is\/somewhere)
(?^:\/unix\/path\/to\/folder\/is\/herewith)
/unix/path/to/folder/is/here
/unix/path/to/folder/is/here
[download]