modifying kernel config in Yocto

It is difficult to answer without seeing the real kernel recipe but what is probably happening is that the kernel recipe for the socfpga only inhertis kernel and not linux-yocto. If that is the case, then you can't change the configuration using fragments, you have to provide a full defconfig.

maybe it is late but...

The kernel development have its own way for making changes. I put one post here yesterday but I understood I am wrong so I erased it immediately. I will not put the exact steps. Just short description. You should find them in yocto dev manual, because it is not something special.

The kernel changes should be made directly on the sources (usually in /workdir/tmp/). And then use git to make patches. If you make changes in configuration using bitbake -c menuconfig virtual/kernel, or other way, put it directly in kernel .bbappend file as you did. That definitely works. I tried with devtool almost the same and the patches were left not merged.

The simple way to make modifying kernel config using menuconfig in Yocto is :-

bitbake -c menuconfig virtual/kernel