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Could you clarify if the domestic violence was against a family member?
Yes that is because the requirements under EU law is different from British law. You can be denied only on the basis of public policy, security and health grounds.
I cannot go into any detail as you have not requested a detailed answer. You can apply for PR once you have 5 years continous residence of treatyrights and not ILR. You can only be refused on the grounds i have already stated and you dont fit into any of the grounds.
Unlikely as you are still together and it was a domestic matter and you said she wanted to withdraw her application.