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Fix two-stage processing when flat node file is used #1908

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Job	Run time
ubuntu22-pg11-clang13	10m 51s
ubuntu22-pg11-clang13-jit	11m 54s
ubuntu22-pg11-gcc10	11m 1s
ubuntu22-pg12-clang14-jit	8m 46s
ubuntu22-pg13-gcc11-jit	9m 3s
ubuntu22-pg11-gcc10-jit	10m 47s
ubuntu22-pg12-clang15-noproj	8m 28s
ubuntu22-pg13-gcc12-release	10m 15s
ubuntu22-pg16-clang15	9m 18s
ubuntu24-pg14-clang16-jit	9m 21s
ubuntu24-pg14-clang17-proj	9m 51s
ubuntu24-pg15-clang17-noproj	9m 39s
ubuntu24-pg15-clang18	9m 11s
ubuntu24-pg16-gcc12-release	10m 39s
ubuntu24-pg17-clang16-cpp20	10m 36s
ubuntu24-pg17-gcc12-cpp20	10m 36s
windows (windows-2019)	29m 50s
windows (windows-2022)	40m 4s
windows (windows-2025)	24m 54s
windows-package	1s
	4h 15m 5s