Somehow I have the feeling that the standard solutions, like te ones proposed here, don't really apply to your problem. I guess that you're actually trying to process in include-like tree, where some lines in a file point to other files, which you want to include as well... Am I right?

In that case, I would think somewhat in this direction:

my @todo = glob('c:/*.inc');  # some kind of file
my %done;
undef $/;
while(@todo) {
    my $file = shift @todo;
    open FILE, "+<$file" or die "Can't open file $file: $!";
    $_ = <FILE>; # whole contents of file
    if(s/\bold\b/new/g) {
        # replace contents of file
        seek FILE, 0, 0;
        truncate FILE, 0;
        print FILE;
    }
    my($dir) = $file =~ m[(.*/)];
    while(/^#include (\S+);/mg) {
        push @todo, "$dir$1" unless $done{"$dir$1"}++;
    }
}
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But I must admit that I haven't actually put this to a test, I only made sure it compiles. It's just to give you some ideas.