Whichever file is named ".config" is the one that will be used when you run make. If you have numerous config files, they will each presumably have slightly different names, with the names indicating some build version or change you've made. For me, for example, if I build numerous kernels of the same kernel version, I add a suffix like -b0, -b1, -b2 etc., to the config filename. Then, if I want to build a particular version or configuration, I either:
1-- start `xconfig`, load the file I want, and save it as .config
or
2-- copy the file I want to use and call it .config
Then run `make clean` and `make` etc..
If you've got numerous kernels built, from different config files, you still can run only one kernel at a time anyway - if you want to try a kernel that was built from a different file, you'll need to reboot.
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