Remove both parts.
Well, there are several reason why it's bad practice in RMXP.
The first thing is that it's ambiguous to the reader. If you have defined A#method1 and B#method1 and then include B in A which method1 is called?
Second would definitely be stuff that is aliased. You simply can't insert code into an already existing method by including a module.
Another two things are that the code usually becomes very confusing and save data problems. Before I made my own caterpillar script, I was using Fukuyama's and those two problems were present. Are you familiar with the term "spaghetti code"? Well, that was what Fukuyama's script looked like. There was a bunch of modules and class and none of them really made sense. Of course, that could have been because the code was maybe badly structured. As for the save data, since module data was saved, all savegames became completely corrupted when I removed the script. With aliasing you have usually two scenarios. One is that you have additional only classes/methods in the code and the other is that you have additional variables that are being saved. With the latter you can still make a piece of code to "repair" all data corruption in the save files after loading (which basically occurs because the variables are set to nil since they weren't there when the save file was created). Editing any methods which includes adding, removing and aliasing does not affect the save data. Including a module in a class, though, will crash it. Of course, if you add new classes to the save data, they will also crash the game if you try to load the data once the script has been removed, but those are quite rare cases as you don't need to save instances of additional class in most cases.