I have similar experiences when communicating with an alter who is new or usually quiet. In my case I get awful headaches, followed by feeling faint and exhausted. I've found that after a few interactions with them that my headache goes away for good. I have 5 alters, and it used to happen with all of them when I was first diagnosed, but now I only get with two of them. I spoke to my therapist, and she told me about how my brain is literally re-wiring itself to deal with this new part of me. I rarely had headaches like that before, so when it started happening when trying to talk with the alters, made me scared. But now I can understand more about things. I hope you get some peace with this too.