By reverting these 5 templates: 1) Any hack that used them will no longer function and 2) All custom edits will be removed; they will go back to vB's default (bluish) style. You'll need to re-apply any custom work that you've put into. That's the only drawback whenever upgrading vB versions.
Since you've already gone over the (50) templates by reverting or by making the necessary changes do so with these last 5 templates. This is to ensure that all of your templates are 3.6 compliant. You've already gone this far. I had too a fully customized site but I've scrapped everything on the site and now in the process of rebuilding from the ground-up.
Hawaii represent. Keep the Aloha spirit alive.