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Need some advice for dealing with my "temporary" small mixed re-home and 16 week old

Hi. I have a bit of a dilemma. I've been caring for my boss's small mixed breed dog, Sophia for the last year. She had to be "temporarily" re-homed because of her situation at home. My boss has a female 2 1/2 year old gsd at home who has attacked Sophia on multiple occasions. My boss had finally started keeping them seperated at all times, but decided to breed the GSD, Nova. The final straw was when she was carrying Sophia into the house, after the GSD became pregnant, and Nova went after them both. Definitely too dangerous for everyone to let Sophia continue to live there.

Sophia gets along well with my 14 year old medium size mix and with most other dogs she's introduced to, regardless of size, but she has a definite problem with German Shepherds. My former puppy, Max and my current puppy, Journey were both well tolerated by her (she played with them both) until their ears stood up. In both cases, she went from being friendly with them to an outright growling, snarling, teeth-baring and sometimes aggressive mess. I realize that it's most likely fear based aggression. None of those behaviors occurred before they started really looking like German Shepherds, and it was instantaneous in both cases.

My question is what to do about it. Do I keep them separated indefinitely? Or is there some way to work through what's going on with her? Neither Max nor Journey were particularly bothered by her behavior. It certainly didn't/hasn't lessened their interest in her, in fact, with both, it seemed to make her more interesting. Max had learned to pretty much ignore her, but he had a super strong ball drive and some serious focus on that. Journey, on the other hand doesn't seem to have as much focus on anything, but he's only 16 weeks at this point, so who knows?

Any advice would be appreciated. I should have asked this question nearly a year ago, with Max, but this was only supposed to be a temporary situation. After a year, however, I'm not so certain it is.

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