In the mean time,I think I found the lines(linux-3.9.3/Makefile) creating
overwriting the config file.
# If .config is newer than include/config/auto.conf, someone tinkered
# with it and forgot to run make oldconfig.
# if auto.conf.cmd is missing then we are probably in a cleaned tree so
# we execute the config step to be sure to catch updated Kconfig files
include/config/%.conf: $(KCONFIG_CONFIG) include/config/auto.conf.cmd
$(Q)$(MAKE) -f $(srctree)/Makefile silentoldconfig
when I comment out above lines the config file was not overwritten.