You show the end of "My local whois server returns output in this format:" as

Hostname:             ns3.dom.ext
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However, the end of your $resp adds two additional \ns. If I remove those from my test code (i.e. my $resp = "... ns3.dom.ext";) the output becomes:

ns1.dom.ext ns2.dom.ext
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which isn't empty but is different.

If I change the end of $regexp, in my test code, from \n) to \n?), the output returns to:

ns1.dom.ext ns2.dom.ext ns3.dom.ext
[download]

So maybe that's something to look at in your code.

In my original response, I wrote 'See "Short, Self-Contained, Correct Example".'; I perhaps should have been more specific and written 'Please supply a "Short, Self-Contained, Correct Example".'.

If you do provide an "SSCCE" which reproduces your problem, along with expected and actual output (as opposed to vague, prosaic descriptions: "contains the expected response", "is empty" and "is fine"), I'll happily take another look. At the moment, I'm just making guesses about what you're not showing us.

You should also read, and follow the guidelines in, "How do I post a question effectively?".