I will check the code soon to see if there's any mistake, but what I know now is that the theme I uploaded only contains a folder with some modifications of the main templates ( /modulename/templates/template.htm ) and not the files related to menu items and their options ( /modulename/*.php or /modulename/lib/.conf ).
I didn't add / edit / remove any menu's, only edited the template files changing the id="" of the main contents, buttons, and <li> and <ul>... all of this shouldn't give you any problems.
To have a more clean panel I suggest you to disable the unused modules from the admin panel. To do that, go to Sistem -> Edit panel users -> and click on the account and uncheck the modules you don't use.
Relogin and you will apreciate the change.