I had the same problem. I already checked the box for the right alliance last week.
After the reset i joined my squad on blue borderlands. ( First haven) I was able to see the other squad members.
After the mini crash i tried to rejoin my squad but suddenly I was on another server and another alliance box was checked. (Phoenix dawn) I selected my alliance first day it was available.. Now I won't be able to join my alliance for the beta.
Support said they sadly couldn't migrate me to the right alliance.