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I start a make -n of big project (multiple directories; Makefile and configure created with autotools); I think that nothing can be changed by this make; but it starts a config.status --recheck and regenerates some Makefiles and config.h.
Why does make -n starts anything?
Have you read the manual? If you look at this section, you will see that recipe lines that start with a
+and ones containing the$(MAKE)variable are always executed. Perhaps your Makefile contains such lines.