I've experienced the same thing in NYC, which also (in)famously changes their courses slightly but enough to necessitate a new cert, as well as some aforementioned events here in CT.
My main concern in this regard is practicality and consistency. Some measurers will be diligent and accurate in reporting courses that "replace" an older one, and some certifiers will send that notice up the chain of command. Others either won't understand the meaning of "replace" (assuming a consensus is reached) or simply won't bother notifying the higher-ups of such a change in status.
And what if a different measurer measures a "replacement" course but isn't made aware that the pre-existing course was certified (or that perhaps its certification simply expired)?
In my view, this just makes more work for the registrar, and may not give us a "better" database - you may have some states that are 99% up to date, while others are full of "replaced" courses in the database.
I see little benefit in changing the status of "replaced" courses at the cost of a lot of clerical work.