I’m using lens flippers to improve my accommodation facility (it takes me 8 minutes to do what should take under 1 minute, now down to 3-4 minutes) and I can really “feel it”, but it’s more like DOMS from the gym, as opposed to “I injured something.” That feeling goes away within an hour or two. I wonder if you could be getting eye pain from too much close work? For me, just 10 minutes of texting on the phone with no plus lenses really does a number on my eyes and messes up my distance vision (accomodative infacility / asthenopia.)
It’s good that everything in your eyes looks fine. You might try some of the various vision therapy activities and see if you can figure out exactly what’s causing that feeling.
Some people have very good luck with eye massage or putting a warm or cool washcloth on closed eyes. If you have allergic issues you might try allergy eye drops. I think @Ashvapathi has had good results from eye wash.
I hope you get it sorted out and feel better soon!
You might also try various colored lenses and see if they do anything for you. Some people who suffer from migraines have relief from pink or green lenses. If you’re under crappy lights at work or getting eye strain from screens, any of those things might be worth experimenting with. Easy stuff to try includes drinking more water, making sure you’re not getting dry eye, etc. Some people swear by blue-blocking lenses (I know @jakey is not impressed), it might be worth trying some yellow or amber lenses and seeing if that helps any too.
Migraines & FL-41 Tinted Lenses | University of Utah Health
Computer vision syndrome | AOA
I would think the doctors you saw would have probably ruled out the things below: