You're right, I didn't read your original code carefully enough.

You can introduce a variable that stores if it's after the STRUC20 line:

while (my $matchingFiles = glob("*.rtsd001")) {
    ...
    my $seen_struct;
    while (<UNMODIFIED>) {
        if ($seen_struct || /STRUCT20/) {
            $seen_struct = 1;
            print MODIFIED $_;
        }
    }
    ...
}
[download]

That way you don't have to store all the rest of the lines in memory, and still get the same semantics.

Update: actually this solution looks more elegant, but does nearly the same thing.