Or maybe they are using a new set of time travel laws, where Eddie killing himself erases his family line, but does not impact what they have already done. So ReverseFlash doesnt exist in the future from THIS time line, but he did in the other and everything he did in that one stands in the current. Killing Barrys mother, creating star labs, the accident, Barry becoming the Flash, ect. That would easily work for me and make sense.
In any case, I really enjoyed the episode and look forward to next season to see how they handle it.