Having that box checked isn't quite as bad as you may be thinking it is.
All it really does is prohibit the AU from overwriting any files in your UI directory that have been modified in one way shape or form to be different from what the AU distributes.
Example 1: The character select/shutdown window (eq2ui_mainhud_shutdown.xml)
Since this window requires the .xml for it to be modified in order to work (with your character names/servers info), having the 'Do Not Update' box checked will allow this file not to be overwritten.
Example 2: Using a mod that is not part of the ThorUI package
Let's say I found a pet window mod that I like, but is not included in the optional mods within the AU. This, like in the above example, will not be overwrote as long as I've got the box checked.
Both of the examples I've given will tag the files with a 'modified date' of whenever the file was last saved in that location. Thus, making the 'newer' in the AU's eyes.
Any other files that you do not modify or swap out will be updated whenever Faeytyl releases new versions of them.
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"Certainty of death! Small chance of success! What are we waiting for?!"
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