Thanks for getting back to us. I did book the flights with LH in the end. So far, I have only the LH reference, and I was planning on trying to keep it that way! I have already chosen seats - I assume that will work.
No real surprises on the miles and the upgrades, but the baggage does sound confusing. I am expecting lounge access based on the airline operator - i.e. EY lounge in AUH, even though it is a LH ticket; I assume that is correct...

I have done this journey several times now (AUH-TLS via FRA, CDG, FCO and BRU) and it is always hit and miss for EY to issue the onward ticket - never had any problems having the bags checked all the way through though, and I have always had a long enough connection that it hasn't been a hassle to collect a ticket. Missing the connection sounds like a problem with the itinerary more than anything else - though I suppose EY shouldn't sell unachievable journeys

The other apparent advantage to booking the tickets through LH was the number of options. You would imagine, and a look at ITA matrix confirms, that there are a lot of options for a AUH-TLS with one stop, but the EY website shows only 2 or 3 a day. The LH website shows more, which is counter-intuitive.

Anyway, I am hoping it works out with LH - I will probably end up doing this journey quite often and it would be useful to find "the way" of doing it, both for my own sanity and to try and get some useful points.

Thanks again for getting back to us.