"Upper" ones do not always go away and I think, usually, they happen about 1 year after you expect to see lower ones.
If possible, I'd have a dentist.
When a mare of mine, Khaki, had what I thought was Upper Tooth Bumps (like you say, started below the eyes), she was only 2yo. I mentioned it to the vet when he was out not expecting any resolution to it at all. He looked and said she had "big head syndrom" which is caused by a calcium / phopsherous (sp?) imbalance.
She'd had colic surgery the year before and was on a diet of mostly hay cubes and soaked beet pulp, per the surgeon.
What we did was put her on a supplement the vet recommended. I don't now remember the name. We also started to give her complete pellets which the vet said was fine for her. Slowly, those upper bumps went away.
THEN, they came back a year or 18 mos later, but at that time, they were just from her teeth growing / shedding. I don't recall now how long this "normal" right of passage lasted, but her head is now normal without any bumps, upper or lower.
Additionally, if you remember "Stacey" who posted here years ago? She had a senior mare named Kat at one point and this mare (silver bay) had these upper tooth bumps. I do not know if it was from an imbalance as we caught and fixed with Khaki, or if it was from some kind of retained teeth issues? But this mare was over 5yo and the situation was beyond being fixed at that stage.
You may be able to google and find information about horses and "big head syndrom". It, of course, has a technical name but this is what my vet called it and when I investigated, I was able to find additional information. I do think with this kind of problem, and with teeth that are not shedding properly, timely intervention is important. Sometimes just a floating will knock the caps off and get things going as they should assuming it is not big head syndrom (which requires supplementation / diet changes).
Here you can see
Triple H Buckin Khaki (buckskin) with these upper tooth bumps (big head sydrom was gone prior to the bumps) and see her "currently" all normal.