Okay. Rather than downloading the whole again, I only wanted to download John's kernel.
So, I changed the local manifest to point to John's kernel (into hybris-12.1 branch) and deleted the kernel folder in the android tree. Then I ran the 'repo sync --fetch-submodules' expecting it to download the kernel into the kernel subfolder. Instead of that, it gave me an error saying the branch 'hybris-12.1' doesn't exist.

Finally, I manually created the kernel/lge/hammerhead folders and manually cloned (git clone) John's kernel into it.

The kernel compiled fine with less warning. So far so good.