Created a new ship class (Colonizer-2) with faster engines. Later on, I went to upgrade it to increase the range, and saved the upgrade (Overwrite=yes, pay upgrade costs).

When I start a new game, there are two Colonizer-2 ship classes available from the quick-build list.

Examining "My Games\GalCiv2\ships" folder, there are three files--not four, not two--related to the Colonizer-2 ship class. Two of them are *.shipcfg files, listing the ship contents, and they have had a sequential number appended to their file name. "SO_UD_Colony-2_0.shipcfg" and "SO_UD_Colony-2_1.shipcfg". The third file is a binary containing the current version, simply labeled "Colony-2.shipclass"