I'm finding now that making changes to my user layer doesn't affect my journal. Any changes I made to my user layer before I adopted the style are perfectly intact; but now, to change something, I have either to use the GUI or make the change to my theme layer instead.
I'm not sure if this behavior is intentional, but it doesn't make much sense to me; why even have a user layer if you can't use it to change things about your journal?