I think some of us are paranoid about green freight cars because of all the green Santa Fe stock cars we've seen produced by every model company that ever produced a stock car, except Intermountain. And I guess BLI, if you call that thing a stock car.
I'm willing to believe EJ&E had green flat cars. They certainly did also have black flat cars, and according to Tichy's graphics that show their decals, they also had brown flat cars. I note that EJ&E seemed to paint every batch of boxcars they had differently- ending up with boxcar red, green, and orange with green cars- so it may have been true that flat cars were treated similarly. I've noted that a couple model companies have also produced green EJ&E gondolas, but all the ones I can find photos of are black.