If you create a new mdb file and then select Insert > Table > Import, you can pull in tables and queries, but nothing else. You can't use the linked table manager from within the mde. You can link new tables from within the mde.
So what you should do is to open the mde, hit f11 to open the database window if it isn't open, then select Insert > Table > Link Table, and link the tables from their new location. And delete the old tables. Use a COPY of the mde to try this with.