In the recent episode S03E06 of Star Trek: Discovery, USS Discovery got lots of upgrades
like detachable warp nacelles held by programmable matter (guess they are going to blow in a future episode) and programmable matter based controls,
but one possibly overlooked major upgrade was its registry number:
(A new letter has been added to USS Discovery's registry number; previously, it was NCC-1031 and now it's NCC-1031-A)
Why did the Federation change the registry number of USS Discovery? Even with the major upgrades, it's the same old ship with Spore Drive unaltered.
Historically, we've seen that a new incremental registry number is assigned to a new ship and that's also when it replaces a destroyed ship of same class. In Star Trek: First Contact movie, when Picard initialized self-destruct sequence of USS Enterprise NCC-1701-E, Picard and Beverly Crusher had this conversation:
Crusher: Think they'll build another one?
Picard: Plenty of letters left in the alphabet.
Talking about Federation's logs according to which USS Discovery was destroyed long ago, the logs can be rectified. Yes, Time Travel was a crime, but Federation was the ultimate authority there. If they trusted USS Discovery and knew that it wasn't involved in temporal war, why couldn't they simply pardon it or change the law?
Why did they change the registry number of USS Discovery?
I want to know answer from both in-universe and out-of-universe perspective.