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emerge --depclean

# emerge --depclean
    selected: 4.4.21
   protected: none
     omitted: 4.4.26

emerge --depclean does not remove the kernel source if you have CONFIG_PROTECT. If you build the kernel in-tree, the kernel source will be removed but all the files created by the build process will be left. Those have to be removed manually:

In fact, it is better to build out-of-tree with $KBUILD_OUTPUT, allowing multiple builds with different configurations.

So, if you want to keep the kernel sources of a specific linux kernel, you might want to add the package to your world file:

emerge --noreplace =gentoo-sources-versiontoprotect
emerge --ask --noreplace gentoo-sources:4.4.21

See also