Most probably is... The dad feels betrayed since the mom kept those secret letters about her crush (or lover?) and its also not helpful that yunifer is so diff than her father (in terms of elements) since during that time its the norm that children will inherit their parents elements...
Only after a research paper talk about the possibility of children having diff element did the dad finally realize that he was influenced by his own feeling and forget that despite everything she is still his daughter that he had abandoned all those times... So i guess blood related or not its probably not the main issue there
I've reread the side stories so many times but is yunnifer and her dad biological father and daughter???