I think there's a few approaches - but the very first step is to work out what you want.
Do you want the old policy back - just for you? Do you want to stop travelling? Do you want cash instead? Would you resign rather than fly Y? The outcome is important here.
If you're willing to put up with it and believe you can manage the travel schedule etc with your health - I'd put your head down and get on with it. Anything else is going to be seen as being difficult by the employer.
But if you want to fight it and put up with the label 'difficult'...
I'd actually start with your employer (go to HR - not your boss) - explain the situation, explain the medical situation and say "Look - this was ok in premium eco because I could stretch/walk/whatever - and that's not possible in economy and I'm worried for my health". That *should* set HR alarm bells ringing. Getting informed about a potential health impact and ignoring it would be a disaster if anything happened to you. Make *sure* it's documented - by you in a follow up email if required ("Just to confirm our conversation ..."). But also make sure it's right - don't go in and say "I get a migraine in economy" if you don't - the worry has to be real.
They might insist on a medical letter - and you can then explore that angle.
The outcome of this might be that they give you an exception from the policy. But I'd guess the more likely outcome would be an attempt to remove you from the need to travel (with them thinking "well - if he's that bad he shouldn't be on a plane anyway") and, honestly, if you were my employee - that'd be my angle - after all - this might not stop here and you might be back next month asking for business class because something happened to your back/leg/head/whatever.
Remember - companies, in that situation, are likely to be thinking "what about the tribunal" in the back of their minds (they shouldn't - but they will). But that means they'll tend to go procedural to ensure they tick all the boxes.
Now - there's another option - IANAL but I'd hazard a guess that if you're Europe based - that'd be a breach of the working time directive (given the ruling on Tyco). Travel time should be included as working time, so if you do 24 hours in the sky + 8 hours working you're at 32 already - you'd only need 2 more days in the office/online that week and you're over. I'd certainly have a crack at the argument if they health angle didn't work.
Most UK companies put some generic "I opt out" clause in your contract - but you're more than welcome to opt back in. Generally would put the cat amongst the pigeons though. But again - unless your travel is critical - I'd suspect they would come and say "well look - if you're not willing/able to do <x> and <x> is the job - we need to find you a different role".
In the grand scheme of things - if you're happy to consider moving on from the company within 12 months - I'd make a bit of a fuss and see what happens.
And to give you two solid examples from my own recent past:
- I needed to do a LH - we're normally WTP direct (and book BA), but the prices were bonkers. The only real option was an Air Transat flight with 1 connection in their 'club' (really PE) cabin - it added 6 hours to a 7 hour journey. I said "no" because I'd hurt my back and I wasn't going to do 13 hours on a 7 hour trip (especially without a lounge!) and the trip was put off. The company understood and re-worked the schedules.
- The company also attempted to put an 'all economy' policy in place. I simply said "Look - I travel enough and I don't need to spend those hours cramped up". There was a bunch of back and forth (including comments about being well paid enough to put up with whatever was thrown at me) which ended with an email from me saying "ok - if that's the policy - that's fine - but we either find me another role that doesn't involve the travel or I guess we're parting ways". Since there wasn't another role for me to do and finding a replacement would be tricky - the policy was amended with an exception clause which myself and (now) the CEO make use of.
However, both incidents have led to me being seen as awkward and stubborn - and my 'star' in the company faded a bit because of it.