Just to clear things up: EN is 100% owned by LH, and LH consideres them part of LH regional, although in some respects they stand out a bit from the other regional partners, e.g. by the different livery, interiors and Italian-style service. They also different in that they actually offer a few flights that are EN and not LH coded, but those are the exception. I wouldn't fear for their existance, they seem to be doing very well in the Nothern-Italy-Germany market and feed the LH lounghaul flights very well.

I really enjoy their service, especially now that I've noticed driving or taking the train from INN to VRN can be absolutely worth it for the long-haul fares from VRN.