"Here's the entire code."

Really? See Re^2: search and replace with a variable. Your "entire code" won't compile because you added use strict; to it before posting, which catches the fact that you misspelled $fqdn on line 27. If it were spelled correctly, the substitution would work as expected. But do read Re^2: search and replace with a variable, because without proper file locking your next bug is only a few web hits away.