Adding this because we ran into a similar problem (not the same upgrade version), but were able to resolve the issue. KVStore wasn't liking our certificates so we stopped splunk, removed the server.pem file and the $SPLUNK_HOME/var/lib/splunk/kvstore/mongo/mongod.lock, and started Splunk. KVStore didn't like our cert and it fixed our issue. Hopefully it helps anyone else stumbling across this thread.
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