Are you trying to send something to the client? I think $r->pool is only freed at the end of the request, so your handler is being called after the content is already sent. The docs indicate $c->pool->cleanup_register should be used "to run a cleanup at the end of each connection phase":

use Apache::Connection ();
use APR::Pool ();
  
$c->pool->cleanup_register(\&my_cleanup);
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Maybe you'll have better luck if you asked this question on the mod_perl mailing list.