I do not have an answer at this time, I will try to get something for your question, in the meantime I will recommend you to verify in the Yocto site as well.
Thanks, once I continued building my image, the headers version of the file seemed to disappear. I ran a full bitbake on our server all the way through, and I only saw the kernel file in the linux-yocto-clanton location, so perhaps the second file was just a residual part of the build process.
Kernel is fully compiled and now loaded onto the board, as soon as I get my serial cable spliced, we'll see if the modified kernel file got compiled in correctly.
As you mentioned it was perhaps a temp or leftover from the build procedure. Let me know how your project goes.