It is usually best to do make mrproper which is a more extensive clean
But it will delete your .config so if you want to keep it, copy it elsewhere then copy it back in.
If you want to compile a kernel using an old .config file, you can do a make oldconfig
So let's say you grab a kernel from ftp.kernel.org. I always do this:
make mrproper make config make dep make bzImage make modules make modules_install
If you save your .config file and want to a completely fresh compile, do
make mrproper
copy the .config to /usr/src/linux
make oldconfig make dep make bzImage make modules make modules_install
-- Doug
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