While it is possible, the most likely thing that happened is that your friend is seronegative, but has Lyme anyway, as this is actually quite common. Sometimes one infection is kind of "hidden" because the levels of bacteria aren't very high, and so the body is only dealing with what's most threatening at that point in time.
In that case, the person should only treat Bartonella and Babesia (assuming they have zero Lyme symptoms), and watch for Lyme symptoms to show up during treatments.
I would suggest that they see a LLMD at least at first, for more direction.
What are the symptoms that are specific to lyme vs one of the coinfections?