@dpsutton I don't understand why, but based on my experiments the kill-process line you pointed to is not the one that kills the nrepl server process. I believe it's this one: https://github.com/clojure-emacs/cider/blob/3e9ed12e8cfbad04d7618e649322765dc9bff5d6/nrepl-client.el#L625

monkeypatching that function to be a NOOP seems to fix my problem