Since you can't load a file sized 3GB into memory, so you have to read it in chunks, examine what is read so far, do your substitutions and write what's processed to another file. There are many ways to do that, here is one:

#!/usr/bin/perl

my $binfile = 'binfile';
my $outfile = 'testfile';

my $re1 = qr{blorf};    # that is the regex which saves the token
my $re2 = qr{foo bar};  # that is the regex for following lines

open my $in,  '<', $binfile or die "'$binfile': $!\n";
open my $out, '>', $outfile or die "'$outfile': $!\n";

my $buf;    # empty
my $found;  # not yet

while(! eof $in) {
    if ($found && /$re2/g) {
        # do substitution
        s/$re2/quux $1 $found/;
    } elsif (/($re1)/g) {
        # if we match the start of a section,
        # we remember what we need and write all things read
        # up to the position of the current match.
        $found = $1;
        my $chunk = substr $_,0,length($1)+pos;
        print $out $chunk;
        substr $_, 0, length($1)+pos,'';
    } else {
        read($in, $buf, 50);
        $_ .= $buf;
    }
}
print $out $_; # spit out last chunk
[download]

I hope that's readable...

See pos, perlre.