And changing the appearance of a ship with significant portions made up of something called “programmable matter” seems easy, it feels like it would be particularly suitable for adaptations.
If I can paint my house the original color in a matter of weeks an old color on a starship should be like changing clothes. I would think at least.
The how is easy, the why would be the contrivance. I can't think of a reason for the ship to return to its 23rd Century appearance that would feel natural and not "because we need to explain the old design used in Calypso".