CGI has a flag that causes subsequent calls to header to be silently ignored.

$CGI::HEADERS_ONCE = 1;
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However, it's only documented in the source, not in the pod. The alternative would be to make your own flag.

if ($cgi_header_already_printed++) {
   warn("Attempting to send second CGI while trying to ...\n");
} else {
   print CGI->header();
}
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