If you make a backup copy of an existing ship file be sure to use a different extension for it. The code looks for all files with the extension .ship (or .SHIP - it is not case sensitive) for ships. Duplicate definitions for the same ship could cause confusion. The same is true for many other extension names, such as .tech for the technology definitions, .anomaly for the anomaly definitions, .imp for the social improvement definitions, .sbmodule for star base module definitions, and .event for colonization events. Do not use these file extension names for anything that you don't want the code to read and be careful to use the correct extension name for the file's content.
p.s., there are two other files called stars.lst, which contains the names of stars the code can choose from, and english.str, which contains a lot of text strings in english. I don't know if these file extensions work the same as the others.