Please note that this article refers to styles by Elevenfour.
TL;DR: Keep it.
Style protection is a feature that's WoltLab's answer to a user suggestion since the early days of WoltLab Suite 1.0 (back then still called WoltLab Community Framework, WCF): Make it possible to upgrade a style directly without having to versions of the style installed in the end.
So, the style protection does exactly this: It protects the designer's (S)CSS from being changed so it doesn't conflict with user's customizations by providing an additional field where the user can enter their own (S)CSS, The latter will be kept when updating the style. Same goes for color settings: these won't be updated, which is a downside if the designer did something wrong which they want to correct later.
Should I disable style protection?
Let's talk about the conequences here first: You won't be able to get direct style updates anymore. If you do update the package file, you'll end up with more than one version of that style. And all your settings from the tab "Own Declarations" will be lost - so back them up first!
If you've intalled a style that doesn't have a package identifier (see the tab "Data") you'll always end up having two or more versions of the style. Direct updates will only work if the style hast the same package identifier. As Alexander Ebert stated: The identifier of the package.xml doesn't matter - it's always the one include in the style.
In most cases it's best to keep the style protection and enter your own (S)CSS under Advanced Settings
If you disabled the style protection you cannot undo this. If you have more questions on this topic feel free to ask in Elevenfour's forum.