Hello again and welcome back, although I'm very sorry about these additional problems.
In trying to offer help to you, we are at the point now where we absolutely need to know exactly which autoimmune disorder your girl has been diagnosed with. Otherwise, we will be endlessly chasing down rabbit holes in terms of both symptoms and treatment. So until we find out that diagnosis, I believe our hands are tied.
In terms of the seizures, however, I do have a couple of comments. First, was the phenobarbital prescribed solely for ten days alone? If so, this seems strange to be. It is a medication that takes time to build up to a therapeutic level in the bloodstream -- typically at least a couple of weeks. So I am not understanding why a short course such as ten days would even be of any value. Also, just as a sidebar, once a dog has been treated for a period of time with phenobarbital, it cannot be stopped cold turkey or else seizures can be triggered simply by stopping the drug. Ten days probably isn't long enough to cause this problem, but I just want to mention that weaning off is necessary if a longer course of the med is ever prescribed.
Also, I find it interesting that your girl had the seizures after the Apoquel was discontinued and not while she was taking it. In that case, I wouldn't think the seizures were a side effect of the medication, but perhaps instead a reaction to the discontinuation of the medication. Since Apoquel is an immunosuppressant, we're back to needing to know the name of your girl's autoimmune disorder. Perhaps it's the case that Apoquel's immunosuppressive properties were somehow inhibiting the seizures during the time period that she was taking the drug.
Marianne