Appreciated this comment, as it's one of the few useful things Google returned when searching for "perl sliding window string replace". I used it to make something similar that uses substr() instead of a regex, and bumps the buffer up if the search string is larger than the window size.

# note: only lightly tested, ymmv
sub sliding_replace {
    my($srcfile,$dstfile,$search,$replace)=@_;
    if (! -e $file) {
        die("File [$file] does not exist\n");
    }
    open(my $src,'<:raw',$srcfile);
    open(my $dst,'>:raw',$dstfile);
    my $winsize=4096;
    my $buf= '';
    while(1) {
        my $bytecount=$src->sysread($buf, $winsize*2, length($buf));
        while (1) {
            my $index=index($buf,$search);
            if ($index > 0) {
                substr($buf,$index,length($search),$replace);
                my $len=$index+length($replace);
                $dst->print(substr($buf,0,$len,''));
            } else {
                $dst->print(substr($buf,0,$winsize,''));
                last;
            }
        }
        last if $bytecount == 0;
    }
    # print any leftovers
    $dst->print($buf);
    $src->close();
    $dst->close();
}
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