Forum ate my reply, so I'll make this quick.
If you can restart the Alpha arc, then it should be fine to do so. The same thing happened to me, with the exception that I finished the arc before switching and simply went through it again afterwards.
If you can't restart the arc, I'd consider contacting support. (edit: or like the below poster has hinted to, you could 'simply' change sides again, finish the arc and switch again)
If you're on Freedom and would like help with the Alpha arc, hit me up with a PM, I'd gladly help you through it.
A little bit of advice: You can mez the Captain (I think he has a mag 10 protection against most control, Confuse and Hold I am sure of). So if you can confuse him, he can do the dirty job of butchering the Honoree pretty quickly (once he's done annihilating the riktis around).
The contacts in hero Ouroboros may look the same, but they're not the same contacts as the ones on the villain side. When you switched to a hero, all your villain missions were abandoned, and your villain contacts were removed from your list until you go back to villain side.
If you had story arcs open (and you had at least one - Mender Ramiel's), they count towards your arc limit. If you had too many arcs open, you won't be able to get ANY new arcs until you go back and finish at least one. It sounds like this is what happened to you.
@Roderick
So until a few hours a go, I was a rogue, and thus a villian. I started my incarnate quest arc got up to the part where you have to deal with Honoree and Holtz, and beat my head against it for a while, before finishing the quests to become a hero.
Now, however, neither lady Grey, nor Mender Ramiel will tell me anything useful. Lady grey just wants to give me her task force, and Ramiel just wants to tell me about being an incarnate, and I have the clue from the quest with honoree in my list. So did I do something wrong, and if so, how do I fix it.