Update on my Thesis/Paper dilemma:

I talked with some colleagues about how I should approach this. My current PI overheard and suggested that I e-mail her to ask for a phone call. Two days after the e-mail no answer yet. As the manuscript was about to be sent after the weekend, I decided to call her. With no luck. Another e-mail from me followed asking her if we can talk after the manuscript is sent. I got a long reply from her telling her point of view. She even mentioned that they thought about not having me on the manuscript, which is super rude. She said that when it comes to her, she doesn't think that the order will change but I could contact all the authors and explain my reasoning.

I asked my current PI if he has time to go over my claims and maybe give me some advice. He did and suggested that I write all the authors without expecting anything to change. So I wrote (with the help of a friend who is a master of the german language) an e-mail as neutral and professional as possible with a clear "fuck you" hidden between the lines. Two days later I got her reply. She detailed her reasoning, got even a little personal in attacking me and said that if they don't hear anything from me, they would send the manuscript.

Ten minutes later I got an e-mail from the head of the department asking for my thesis to read.

I decided to not respond to the e-mail. I knew that I will not be able to change her mind but I also couldn't just let this happen.