The Other Darrin: There appears to be two ships named Arcadia. One blue (seen in the 1978 series), and the other green, seen in all other subsequent series. None of the stories or animation supports the common fanon supposition that that the Arcadia was at any point destroyed and rebuilt. Or that the second Arcadia is just a newer, upgraded version of the first. Their existence actually nothing more than marketing.
cornponeflicks.org explains it this way:
Takara owned the rights to model kits from Space Pirate, and Bandai owned the model rights to Galaxy Express 999. When the Arcadia was slated to appear in the first 999 film while Space Pirate was still on the air, it would've amounted to free advertising for Takara; therefore Bandai had Studio Nue design an alternate version for them, to avoid giving their primary competition any leg up. (Studio Nue had also designed the blue Arcadia, and would shortly gain fame for its Macross design work.) In its own way, it's not far removed from having two different actors portray the same character in two different TV seasons or movies, in which cases viewers rarely have to contrive wild notions of secret plastic surgery in order to deal with it.