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Does your project use the folder method or the group method? See Create project from an existing directory tree?
I guess, you use the folder method and the directory you don't want is a subdirectory. You can run Find In Files with options Project Files and Results to Edit Window selected with an empty search string to get a list of all project files as %fi in the Ctags option also produce.
Alternatively you can remove from the Ctags options in the project settings dialog the -L %fi parameter (see in help of UltraEdit the page Ctags support) and specify your own include and exclude filters. I think (but never tested), if a file with a list of files is used, Ctags does not apply the exclude parameter on this list. It's also possible that you have not specified the exclude parameter correct.