Jimmy,
I think I know what you mean, but that applies only if you are tinkering with the default theme and templates, but you shouldn't as you are supposed to create another theme set, set it as the default theme for everyone else to view and modify that one leaving the default theme and template set unaffected. When upgrading the only thing to worry about is backing up your custom theme, that's all.
To my understanding this is the way to go without worrying it will do any damage to anything else, this is why SMF offers dozens of themes out there because they do not use the default template and theme, they use their own usually based off the default and therefore do not have anything in conjunction with the default theme and template set.