I would expect that longhaul traffic will be redistributed between the 5 LH group hubs and it remains to be seen what's left for ZRH. I remember reading in an interview with the previous LX CEO that only 5 l/h routes out of ZRH would be viable without feeding by the STAR alliance group. Maybe LX will keep these 5 longhaul routes ( I don't know which ones these are ) and all other ones could be up for redistribution among the 5 LH group hubs. If feeding is the only way to make a longhaul flight viable, it can easily be operated out of MUC, FRA or even VIE and BRU. Ok, this is the worst case scenario and I'm sure it won't come to that, but as all LH group hubs will be struggling for some time to come, I could easuily see LH to prioritise FRA and MUC.
One route I expect to go and not come back for a long time will be GVA/JFK, probably substitued with a code share on UA should they return to GVA.
The five routes that were mentioned in that interview refer to the old rule of thumb in long haul air services, that a route needs 100'000 local PAX per year to be viable, if you don't have any feeders for it. For decades there used to be 4: New York, Singapore, Hong Kong and Bangkok. Nice to learn, that another one went over that limit - I guess it is Dubai, if I have a look at the 2019 numbers (2020 isn't actually accurate for some well known reason). Or they counted in Tel Aviv, which is not actually a long haul ex Switzerland but flown by LX's long haul fleet.
Problem No.1: there are many routes that are just slightly under that limit. Wild guess about the numbers, but does it makes more sense to feed 15'000 PAX per year from all over the world into Zurich to fill a route to let's say Tokyo? Or makes it more sense to hub 85'000 Swiss people via FRA? And this 19 times for all of LX's 24 pre-Covid long haul destinations?
Problem No.2: LX isn't alone on these 5 routes, so even those aren't actually viable for them without transferring PAX. Maybe New York would work. So one can basically argument, that there is no actual need for LX long hauls at all.
Problem No.3: if you do so and leave LX with only European destinations, it will go the way a Malev has gone. There are other airlines, that can do this better, read cheaper on short haul routes. You know them, their aircraft are usually painted in orange, pink or yellow&blue.
We have to take into account here, that even as 5 routes doesn't sounds like much, with this number Zurich is on the 9th position in Europe, ahead of places like Lisbon (4 destinations), Moscow (4), Istanbul (3) and even Munich (2). There are just 8 cities ahead of Zurich (London/65 destinations, Frankfurt/45, Paris/18, Amsterdam/15, Madrid/12, Rome/6, Manchester/6, Milan/5) And there are just a mere 28 other Cities in Europe that can support two or even just one long haul destination. So Zurich is in a quite good position for a long haul hub, in fact number two within the Lufthansa-group and much better suited than Brussels or Vienna. Or even Munich. This is something, even a lot of so-called "experts" often tend to forget about. You can figure out for yourself how "easily" the Swiss passengers can be redistributed via VIE or BRU and how this should make sense.
I also expect GVA-JFK to stay: this route is heavily used by diplomatic passengers with the UNO headquarter in New York and lot of UN-organizations situated in Geneva. There is no reason to give away one of the most profitable routes in the whole group an let UA earn all the money. In fact, some even say, it is the only route in the whole Lufthansa group where the first class actually makes a profit...
Cabin mods aren't really a major factor in an airline's decision (generally) to remove a type, notably if the size of the sub fleet is small. Delta got rid of 18 newly modified 777s and did that very quickly. I'd agree with you that the lift/payload is a factor here, as Swiss is flying a lot more cargo long haul than passenger right now, and yes the 340s have more range than the 330s. As to fuel, maintenance, parts, etc...4 x the number of engines add to the expense.
This - and the fact, that LX has plans for later that year, that include to cut the first class in half and introduce a premium economy product. So the modified cabins in the A340's are already wasted and would have to be modified again anyway. So the new cabins off the A340's aren't actually a valid argument.