As with all instances in which one pokémon has trouble integrating with their team, it’s important to ensure that you have all the information about what’s going on correct. That is to say, it’s worth observing your team for just a bit longer to see if your swablu’s behavior is definitely because of her anxiety and not due to some other issue that may need to be resolved (such as some level of hostility or disinterest from your togekiss or houndoom).
If this issue is indeed caused by swablu’s nervousness, start slowly. Try to keep your togekiss and houndoom away from your swablu at first. Use their poké balls if you have to, but the important thing is, if at all possible, try to avoid exposing your swablu to the both of them at the same time, especially at times when you can’t keep an eye on them.
Now, for your first step, I would recommend introducing your swablu to togekiss first, as togekiss in general have nurturing dispositions and an innate urge to make others happy. To set up the introduction, have your bulbasaur stand by swablu and use Sweet Scent to keep her calm. Explain to your swablu what’s about to happen and who your togekiss is to both you and your bulbasaur. (That is to say, emphasize that your togekiss is a friend.) Take a few steps back, enough to ensure that there’s plenty of space between you and your pokémon, and release your togekiss next to you, rather than between yourself and your swablu. Do not have your togekiss block your swablu’s view of you.
If your togekiss knows Heal Bell, now would be a good time to use it. I know that sounds odd, but the soothing tones of Heal Bell can possibly calm and entrance your swablu, even if she doesn’t suffer from any specific ailment. If your togekiss doesn’t know Heal Bell, don’t worry. This is just a helpful tip, not something that’s absolutely vital to bridging the gap between your swablu and togekiss.
From there, as with most instances in which one of your team members is terrified of another, begin with short, simple interactions, perhaps led by your bulbasaur. Have your bulbasaur interact with your togekiss first. Let him converse with your togekiss and then draw your swablu into the conversation naturally. Allow your togekiss and swablu to have a short conversation with each other, then end the session by withdrawing your togekiss back into its ball to show your swablu that you have the ability to ensure that none of your pokémon hurt her. If at any point, she attempts to attack your togekiss anyway, have your bulbasaur calm her down with Sweet Scent or by using a gentle Vine Whip to hold her back (by wrapping her, not hitting her).
Once your swablu is able to handle short, friendly conversations with your togekiss on her own, give your togekiss more time to interact with her. Additionally, at the start of each session, work your way closer and closer to your swablu until you’re able to release your togekiss within beak’s reach of her. If she isn’t startled by your togekiss’s presence then, graduate to using the two of them side-by-side in double battles or sparring sessions to reinforce the bond between them.
Due to houndoom’s rougher nature, it’s unwise to introduce it to your swablu until after she’s absolutely comfortable with your togekiss. Once she reaches that point, perform the exact same steps with your houndoom, only have your togekiss be present for the introduction as well. Thus, place your togekiss and bulbasaur next to your swablu, give yourself enough space, release your houndoom next to you, and begin by having either your bulbasaur or your togekiss (or both) interact with your houndoom. There’s a good chance that your swablu, at this point, will recognize this process and understand on some level that you’re attempting to introduce her to a friend, but don’t assume that having her interact with houndoom will be any easier. Take it slow and let your swablu tell you when she’s comfortable enough to proceed to the next step.
In other words, the most important thing here is that your houndoom and your togekiss are parts of her team now, and team dynamics are vital, both on and off the battlefield. They may even be vital to your swablu’s ability to heal from her past. Thus, there is likely no way around introducing her to the rest of her team, but with enough patience and time, you may be able to coax her to connect with your other pokémon.