This will not break the existent relationships ?
My method will not, yours might. Let's say you are replacing TableA. If you copy over the top with the same name, select 'Ok' in the warning that appears, then the relationships remain the same. TableA always existed in the database and was always named TableA.
If you rename TableA to copyTableA, then paste in your new table with the name TableA, Access probably autoupdated everything and pointed it to copyTableA. When you rename a table with relationships or used by a form, query or report, it helps you out by updating everything with the new name. So when you paste in TableA after the renaming it stands alone because all those forms, queries and reports have changed to look for copyTableA.
Again, though linked tables would be the best way probably.