When a file is dropped in override I believe it overrides any file the game looks for by that name. Modules can have files inside of them that have the same names as files in other modules. TSLPatcher can inject files into modules such that the injected file won't interfere with any other file by that name, like files that may exist in other modules. When the file p_bastila001.utc is put into the override folder, that file will be loaded anytime the game looks for a file with that name.
Anyways I am sure that is the difference causing you an issue. As to why she turns invisible, I don't know. I would extract the p_bastila001.utc from lev_m40aa and compare them.