The EQ2MAP updater should only touch files associated with the map. That shouldn't have a problem with custom UIs in most cases.
To see what it changes, edit your eq2.ini to have it install into a blank folder (IE, EQ2MAP) instead of one of your UI folders. All the files you see there are all that it changes.
To help you more, you'll have to tell us what you mean by changed. How did your UI change? Did the font change or disappear? Are images gone and replaced with black boxes?
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