... the game keeps complaining that the civ.exe is an unknown version and it refuses to modify terrain. ...
Do you seethe following two error message:
Fatal Error: Unknown Civilization Version !!!!!!
If you want to use civ_map, then try another Civilization version !
Please send a mail to the author !
Sorry, no changes of row 0 and 1 allowed !!!!!!
(that would confuse the data search function)
If you see the above error message then Civilization Map Changer could not find the beginning of the MAP data area. My reading of the notes and code of Civilization Map Changer indicate that the map area can be in different areas of memory (I assume for the different version of CIV DOS). The program locates the map data by looking for a pattern that appears to be the artic. The program requires that the first two rows have the pattern that is unique to the artic. Why the spaceship landing would modify this is unknown to me.
...However, starting my "backup" save of the same game works fine, as does starting a new game. ...
Your meaning here is unclear to me. Do you mean before the landing?
The only suggestion I can make, and it is conditional. If you haven't modify the special resource on the map is to go to an unmodified version of CIV to continue the game.