Here is my current scenario.
You can merge master to production and production to master. However, after every merge, you have to reset the working tree of the folders in question. Here is how you can do this.
git checkout production
git merge --no-commit --no-ff master
git reset /path/to/[.ebextensions and .elasticbeanstalk]/folders
git commit
git push
Also, you may forget to reset after every merge so I suggest you set up a post-merge
hook to do this automatically for the respective branches after every merge.