You're very right. Kerry threw the medals, not the citations, away. Unless he'd lost the original citation, he'd have no need to get new citations.
Hell, I bought all my medals and ribbons four or five times over as they wore out, or to have one set for my blues and another for my greens, etc. Getting a new set of the actual medals or ribbons is trivial. Getting a new citation... that's just bizarre.
I suspect that bureaucratically, the current SECNAV had to sign a duplicate citation to get the replacment medals issued. As I indicated in post #633, my take is that Kerry requested replacement medals and due to the fact that Kerry was no longer an active duty service member, administrative requirements mandated that SECNAV's office had to approve the issue of the replacements once it was verified from official records that Kerry had actually earned them.
Kerry would have been smart not to release the Lehman signed certificates. I guess he figured no one would pick it up and connect it to his latest denial that he threw his medals away. I hope the GOP drops this on him later in the campaign. An October surprise.