Question about hosting on GitHub

I currently have a Jekyll powered blog on GitHub: http://tech.johnpaulwohlscheid.work. You can see the Github repo here: https://github.com/JohnBlood/johnblood.github.io. My question is: can I just replace the content of my repo with the contents of my public folder? (I mean after I get everything working.)

Just commit your content to the gh-pages branch. GitHub deploy the changes automatically.

So, will GitHub then overwrite the Jekyll content?

My question is: can I just replace the content of my repo with the contents of my public folder? (I mean after I get everything working.)

Yes you can. You would just add a new commit. Since you’re using Git you can always jump back to the previous commit with all Jekyll files. The replacement would delete your Jekyll setup but you can always restore it.