It looks like you're installing styles a little wonky. Here's what you should actually do:
Install the style you want - for example, UI.X Dark. Then, create a child style with UI.X Dark as the parent style (note: You can name your child style whatever you like). You won't install a second version of UI.X Dark as the style, but actually create a new style using the "Create Style" button in the upper-right.
Make UI.X Dark unselectable for regular users (the toggle next to the style), and set the child style you created as your default style (assuming you want it to be the default style).
Make sure to put ALL changes - Style Properties and template edits - within that child style.
Now, any time you update your style, you'll just overwrite the parent style with the updated XML.
If you installed via the UIX addon or install & upgrade, when you update the style it'll automatically update the parent style for you (plus create a child style).