All you need is to get rid of the last blank before you use the concatenated IP's;

open(SESIP2, ">sesip2");

open(MYINPUTFILE, "sesip1");
my $line = <MYINPUTFILE>;

while (<MYINPUTFILE>) { 
    my($line) = $_;
    chomp($line);
    print SESIP2 " $line"; 
    }

close(MYINPUTFILE);
close(SESIP2);

open(SESIP3, ">sesip3");

open(MYINPUTFILE, "sesip2");

while (<MYINPUTFILE>) { 
    my($line) = $_;
    chomp($line); # this is the added line <----------
    print SESIP3 "dest \($line\)"; 
    }

close(MYINPUTFILE);
close(SESIP3);
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