Assuming file 1 is always a superset of file 2 the following does the trick:

#!/usr/bin/perl
use strict;
use warnings;

my $str1 = <<STR;
A
B
C
D
E
F
G
STR

my $str2 = <<STR;
B
D
E
G
STR

open my $in1, '<', \$str1;
open my $in2, '<', \$str2;

while (! eof $in1) {
    my $line2 = <$in2>;
    my $line1;

    print "blank line goes here!!\n" 
        while defined ($line1 = <$in1>)
            && (! defined ($line2) || $line1 ne $line2);

    print $line2 if defined $line2;
}
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Prints:

blank line goes here!!
B
blank line goes here!!
D
E
blank line goes here!!
G
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