You are correct. Apparently, Kerry must have requested new medals for what reason we do not know.
I think you are confusing his "medals" with his "medal citations". The medals are made of cloth and metal and are easily replaced by visiting an Army/Air Force or Navy Exchange uniform shop. You may have to show proof that you earned them (DD form 214), but they will sell them to you. If you are in a job that requires you to wear your medals often they get dirty and wear out. They are easily replaced.
The medal citation is the piece of paper that is awarded with the medal and it details why the medal was awarded and it is signed by the issuing authority.
The question is:
Why were Kerry's citations rewritten and signed years after his service ended?