How do you approach a tumor that has been reported as HER2 amplified based on IHC 3+, but further testing with FISH is negative?

Treat as Her2 positive. There is no need to do a FISH test if IHC is 3+. Positivity by either method has shown benefit.  

If IHC is on a core, then I would want to verify by FISH, and test resection specimen to avoid the pitfall of calling HER2+ disease when it is actually a false-positive, especially when we don't review path ourselves. Some clues are low grade, high ER and PR, low proliferation. If HER2+, these tend to be low amplification if anything and HER2 staining might be heterogeneous. 

Oncotype DS on occasion can confirm or deny HER2 status along with risk score if there is remaining doubt.

I would start by repeating the test, and often at another lab. Just to be sure that the results are robust. We often see discrepancies from lab to lab. If confirmed, i would treat as Her-2 Positive if the IHC was truly 3+. Many of the patients that were enrolled on the trials that led to FDA approval only required 3+IHC or FISH. 

ASCO/CAP just released their updated guidelines

http://ascopubs.org/doi/full/10.1200/JCO.2018.77.8738