Well after some tinkering I am convinced that TU-EMPTY.GDB is/was intended to be a GDB file created during install or when you select Ref Mode and select Personal as your starting Universe. When you try to create it with Manager it comes back as an error saying that the file name is already in use. Yet there is no such file found anywhere - the program hasn't created it and neither has the user.
Basically the TU-EMPTY is supposed to be just as the name indicates, an empty Universe Database file ready for you to fill sector by sector via import or by hand.
To get around this problem I simply copied TU-SAMPLE.GDB to TU-EMPTY.GDB.
I could have just as easily copied it to TU-MYSTUFF.GDB and labeled it "My Universe". But when you do this, copy the sample over to your new file so you can edit to your hearts content and keep the sample file intact, you must Register it in Manager. If you copy the TU-SAMPLE to TU-EMPTY, since that name is already registered you can go right into Universe and select "Personal" since "Personal" is the label that has been given by default to the TU-EMPTY.GDB.
I have yet to try to create a truly empty GDB file since this quick work-around does fine. However since your new Universe GDB file has all the Sample data in it, you must decide on what you wish to do with all that sector data before proceeding. You can go in and wipe out all the Sectors, one by one, by right clicking on the sector and choosing to delete the sector from the database or you can keep the sectors in tact and replace only those that you want to replace one at a time as needed. To do this, just choose the sector you wish to replace with your own and right click on it. Choose to delete it and do so. Then right click on the blank sector space and choose import sector. Remember to add the proper coordinates and soon your new home made sector should be where the old original sector once was.