Active galactic nuclei with relativistic jets closely aligned to the line of sight—so-called blazars—dominate the observed sky above energies of hundreds MeV. However, there is still considerable debate about where and how the gamma rays are produced in the jets. At least in flat spectrum radio quasars (FSRQs), a sub-class of blazars, the location of the gamma-ray emission can be constrained. In these sources, optical and UV emission lines should strongly attenuate the gamma-ray flux if the gamma rays are produced close to the central super-massive black holes. Using a newly developed un-biased method to identify flaring states, I will show how Fermi-LAT observations can be used to place limits on the distance of the gamma-ray emitting region to the black hole. I will also highlight recent observations of FSRQ flares with the Fermi LAT and Cherenkov telescopes and present first results on trying to reconcile the gamma-ray variability with particle acceleration through magnetic reconnection.