I already did some changes to the map in past with Ace permission.
If one of you can make a list of all changes needed I can discuss it with Ace an see what we can do.
Please remember that I can work only on the final images (no layers...it's a long story) so please don't be too pretentious!
(... a year later. Sorry I don't think about these things until I play the map again and am bothered by the same problem)
I'm not sure what the best way of going about it would be, especially since you don't have access to the layered file. I think what I would do is just erase the word "ship's" from the bottom right side of the key in the bottom left corner. Then it would say that flags "Denote ownership" while removing the confusing reference to ships. That might be the easiest fix.
The best solution would be to note somewhere on the map the difference between ships and invasion craft. I think the best and simplest solution had this been done by the original author would be to replace the text in that same legend with "Denotes ownership and ships and invasion craft," thus indicating that these are distinct things.