Your changes to the .emp files won't affect AI or any routines. So you can go ahead and change them as you like.
The only thing about these .emp files is that they contain some special strategies for that specific empire (in this case Xi'Chung and Sergetti - I don't know about other empires in the mod). If you add empire using these .emp files, the empire will use these strategies as well. You can mod Xi'Chung and Sergetti .emp files (and save them after that) without fear, because that won't change special strategies located in them.