Hi, I am not a profiling expert and ceased to be an Apache expert about 15 years ago, but I'm not sure your approach will work, depending on where in your stack you are calling it.

From the doc on threaded/multiprocess programs:

Devel::NYTProf is not currently thread safe or multiplicity safe. If you'd be interested in helping to fix that then please get in touch with us. Meanwhile, profiling is disabled when a thread is created, and NYTProf tries to ignore any activity from perl interpreters other than the first one that loaded it.

... but on the other hand, the doc for `endatexit` says:

Sets the PERL_EXIT_DESTRUCT_END flag in the PL_exit_flags of the perl interpreter. This makes perl run END blocks in perl_destruct() instead of perl_run() which may help in cases, like Apache, where perl is embedded but perl_run() isn't called.

I don't know why your output files are disappearing, but note that the default output location for the files is the current directory.

Hope this helps!