Scyther can sometimes be difficult to reach emotionally because of their proud natures and vastly different social norms. The reason I bring this up is simply because while I would normally say “employ team building exercises,” that might not work in this case. The fact that your scyther refuses to be in the same room as your flareon only makes matters more complicated.
What you should do first is work on getting her to trust you. Since she’s a recent capture, you’ll need to bond with her until she respects you and trusts your decisions. If you can establish yourself as the leader of your team (directing her through battles is usually the quickest way to do this), then she’ll be more willing to listen to you if you tell her she shouldn’t worry about another pokémon under your command. Not only will she take your advice to heart because you’re her leader, but she’ll also be convinced you have control over your flareon too.
But to reinforce this, if you have any other pokémon on your team, introduce them to her first, before you try again with your flareon. Have her work alongside them, and let her watch you command them during battle as well. The more she understands how your team structure works by interacting with the rest of your team and by watching you interact with them, the more she’ll understand that the team structure comes first.
In other words, your main goal is to emphasize that there is a hierarchy and that it works, and you should do this largely just by being a trainer and commanding her and your team through battles. While scyther aren’t exactly hive pokémon (they live in swarms and have swarm leaders, but these work like mammal packs, not insect hives), they respect social structure, even those set by humans, and they think in terms of that and seek out strong leaders as a result. Therefore, if you establish that there’s a social structure within your “swarm,” your scyther will assume that all other members of her new swarm obey you to the letter—or, in other words, she’ll believe that the other members of your swarm are perfectly safe because they can’t attack her without putting the swarm structure at risk.
Once it looks like she’s beginning to trust you and understand that her team is basically her new swarm (you’ll know by watching for any signs of respect from her, such as keeping her eyes on you and bending her knees to make herself look smaller than you), it should be safe to reintroduce her to your flareon. She’ll very likely still be a little bit wary around him, so it’s important that you keep watch over them until they feel more comfortable with each other. It may also help to reintroduce them in a place where there’s plenty of space, rather than indoors. This will give your scyther plenty of room to back away if she still feels too threatened to warm up to your flareon. (Forgive the pun.)
Best of luck, anonymous.
The Pokédex According to Bill 