Will WordPress Update effect my custom theme

Solution:

WordPress Codex gives a warning about updates.

That being said, if you look at the “Extended Instructions” for updating, it lists files and folders you can delete. It also lists files and folders you SHOULD NOT DELETE. Those “DO NOT DELETE” items are the files and folders not touched by an update.

So… you should ask yourself, “Will I ever need to edit/enhance one of those core files that may be replaced?”

The answer could help you build safer and smarter.