open( my $fh => '+<', $your_file ) or die "ack: $!";

## read up to a point
read_stuff() or last while <$fh>;

## remember where you were
my $last_pos     = tell $fh;
my $rest_of_file = do { local $/; <$fh> };

$rest_of_file =~ s<$a_regex>($replace);

## go back to where you were
seek $fh => $last_pos, 0;

print {$fh} $rest_of_file;

close $fh;