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I've had a similar situation where my gf will absolutely not ride in primary position no matter how much I explain it's safer to do so to avoid being doored or dangerously passed by. She can't get past the fact that she's in the middle of the road and feels exposed/inconveniencing other road users. However, when being told by someone other than me to do this she seems to have taken on board as something that other cyclists consider to be the 'done thing', and thankfully shes begrudgingly doing it. Sometimes some external influence can help a lot haha.
Not that I doubt your abilities, but - and this is not the forum joke - has she considered cycle training?
She could get an objective opinion from someone who is not her partner which may help.
As an aside, I've often felt that riding with a partner in traffic often results in more aggression than when I'm solo.