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PKHex should generate any files it needs. I don't know why you are having issues, sorry.

There's a reason why I said don't use Gen 3. Gen 3 Pokémon PID-IVs-Nature values are connected, so you cannot just change one and ignore the rest. Since you're new to PKHeX, I'm guessing you don't know how to correct it. [We have a guide here, but it might be too advanced for you presently, hence why I recommended against it.] Okay. Advice I can give you: do not create a Pokémon from scratch. It is easier to modify something that exist. Use Pokémon files originating from the correct generation. Here's a mini-guide for your situation. 1. Download a Gen 2 save from here. 2. Open the Gen 2 save, and drag the Butterfree icon onto your Desktop. (It should be a .pk2 file) 3. Now open your Gen 7 save, and drag the Butterfree .pk2 into the save. Now you have a Gen 2 Butterfree in your Gen 7 save. All you have to do is change the Trainer Name, Trainer ID, Moves. It's definitely possible, using the steps I've described above. Image below shows a Butterfree from Gen 2 that I just edited. If you're not getting it, it'll be because you're doing something wrong.

Like I said, it can only be learned in a Gen II or Gen III game. So making it a relearn move will still make it illegal. If you're new to PKHeX, I recommend setting the origin game to Gold, Silver or Crystal, as it is less complicated. After that, just solve the legality flags that will show up. Do some trial and error, so that you familiarize yourself with PKHeX.

@Ragolay what is the origin game shown on your Butterfree? (See the arrow in the image below) I'm assuming the origin game is either a Gen 6 or Gen 7 game, due to your Butterfree having relearn moves. Butterfree only learns Nightmare in Gen II or Gen III. Hence why PKHeX says it cannot know Nightmare, because origin game is wrong. Also our site communicates via English. I'll try to keep my answers simple, so that it works with translator programs.

After following my instructions try right clicking and Run as Administrator (shield icon) to open PKHex.exe It is quite possible you don't have proper permissions. For example, is this a work computer controlled by an IT department? Are you on a virtual profile? Is the computer locked down in any way? Do you have elevation permissions (run applications as admin?) Another example, It is common for a work laptop to need to be connected to the work network in order to access your profile from the windows server. If you are not at work then you will not have access to your profile and you will not have any icons on your desktop or be able to create local app data folders and files.