Download the mod and do a folder compare against the data directory of the mod and the data directory of your install.
In none of the files that will change are the ones you changed, then it should be no issue.
The settings for enemy craft are not part of your save file.
if a few files are going to overwrite your files, you can compare those files individually to see what changes and apply as needed.
I've been doing this for a while now ever since I figured out that mods step all over each other.
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