By selecting all of your text (not highlighting, that is something different) and changing the options, you changed them for all of you text. A quick way to select all text in the body of a document is Ctrl+A.

When non-printing characters are displayed, a little black square will appear in the left margin of paragraphs where either of these options have been checked. Looking at your document, it appears they still are applied in your footers. This leads me to suspect that they are a part of your normal style. If that is the case, it is likely that they will be checked in at least some future text.

(They didn't get changed in the footers because the footers are not part of the body of the document; they were not selected earlier.)