[tlasjr]

Do I think it needs to be renamed no. But if you're going to, I like the Colby. Keel haul must be dead by now, right?
The other twonsuggestions would be the HMS Diana Spencer or HMS Riki Tili Tavi.

[Superbad]

I think it depends on the nature of the customization and if your Joeverse contains multiple aircraft carriers. The USS Flagg is relatively unique in that it is a singular vehicle with a specific name. In every iteration of GI Joe there are many Skystrikers, HISS Tanks, etc. but as far as I'm aware the Flagg has never been portrayed as just one of multiple Flagg-class aircraft carriers commissioned. If the Joes were to acquire another carrier, even of the same class, it would naturally be given another proper name in accordance with the naming conventions of the real-world military the franchise was inspired by and often directly based on (in this case, the Nimitz-class ships). Also, the general appearance of the ship is iconic and any alternate version should still be instantly recognizable -- if you were to create or customize a Corellian freighter in a way that renders it lacking the distinctive features of the Millennium Falcon, it would be odd to present it as the Falcon.

Given the expected cost of a similarly sized & detailed toy in today's market, it would be appropriate to call any new version the USS Inflation.