use Fcntl ':flock';
my @regexen;
{
    open my $rx, '<', '/path/to/junk.txt'
      or die $!;
    @regexen = map {
        chomp;
        qr/\Q$_\E/
    } <$rx>;
    close $rx
      or die $!;
}

for (@list_of_files) {
    local $/;
    open my $fh, '+<', $_
      or warn $! and next;
    flock $fh, LOCK_EX;
    my $contents = <$fh>;
    # study $contents;  # may want to try this
    $contents =~ s/$_//g for @regexen;
    seek $fh, 0, 0;
    print $fh $contents
      or warn $! and next;
    close $fh
      or warn $! and next;
}