Fix correctness, sanity check, and resolve shutdown issue. #2290

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Run time

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Job	Run time
macOS [lmdb]	30m 19s
Linux [lmdb \| gcc]	38m 20s
macOS [rocksdb]	32m 22s
Windows [lmdb]	57m 9s
Linux [lmdb \| clang]	37m 2s
Windows [rocksdb]	1h 10m 10s
Linux [rocksdb \| gcc]	42m 40s
Linux [rocksdb \| clang]	43m 38s
	5h 51m 40s