I feel like such an asshole. When I lived in Shithole USA there was an out and proud lesbian who helped me accept that I was lesbian too. We became best friends and we moved to a more liberal city together. Recently they came out as a trans man to me. And I'm happy for him, I really am. I can tell he us so much happier when he's himself around me. But when I think about "him", my first thought is always that we're not lesbuddies anymore. I haven't told him, because it's obviously transphobic.
Based purely only on what you’ve told me, I don’t know if this is transphobic as much as it is grieving change.
As far as you knew, you guys used to be the same. Two peas in a pod, two lesbians from Shithole USA who escaped together. There was almost certainly security and comfort in sharing that identity together.
Now, you’ve found out that what you believed is wrong: he’s trans and you’re still a lesbian. You’re not the same anymore. You’re no longer two peas in a pod. Sure, you’re still close, you’re both still queer - but you don’t share that identity like you used to.
Dude, it’s natural to be sad about that. Being sad that your buddy and you don’t share the same identity anymore is okay, it’s not transphobic. You can be super support and love trans folks and be sad you no longer share the same identity as your friend.
It’s okay to grieve over this. It’s okay to feel sad. Change is difficult, and finding out your friend isn’t the same as you can make you feel very alone.
If it helps, he’s probably feeling alone and different as well - he’s probably also sad he doesn’t share the same identity as his best friend any more. Perhaps you can bond over no longer being the same and feeling a bit alone as a result?