If a new mod has a file conflict with an existing activated mod, JSGME warns you. You then have a few choices; but no matter what you do JSGME prevents your damaging your install since you can reverse the changes at will.
In general, most over-writes are harmless, but some will do real damage to the over-written mod. Most cosmetic mods are harmless. Most mods that over-write the menu 1064 and the campaign files will really screw things up. (Thank you Winston
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As you become more familiar with the files of the game and the mods, you will be able to analyze the files and see what the problems are. You will then be able to merge the files; if possible, choose what you want to change or reject the changes.
Modding makes the PC games much more interesting than the console games. Have at it!
Congratulations Dan and Lisa
