I can help clear some things up on this one. I've worn hearing aids for almost 30 years now so I'm very familiar with things in one's ears causing discomfort.
What you are experiencing is your body reacting to a poor fit and/or material sensitivity. Doesn't matter if you've worn them for years, one day your body will decide things aren't kosher anymore. (And actually, the shape of one's ear canal does change over time.)
I can't stress enough that if you spend a lot of time with plugs in your ears, they need to be the custom made kind from an ear doctor. Besides the huge comfort improvement, they also provide better isolation and sq. Heck, even the koss plugs sound hugely better through earmolds. And if you do opt for the custom plugs, make *very* sure you specify that they make them with soft material, which will be a kind of silicone. Left to their own devices, ear doctors would rather people use lucite molds, which are very hard and can become quite painful. And trust me - you don't *ever* want to get hit in the ear with those things in. Seriously painful. The downside of the soft molds is that they will very gradually shrink. I replace mine about every six months or so due to that, but you guys would likely get a year from them. Well worth the $100 or so.
Also, If you spend any amount of time during the day with plugs in, I don't recommend sleeping with them as well. Your canals do need a break. (I never sleep with the aids in, can't actually.) If you need noise to fall asleep, try one of those white noise things for the nightstand.
Hth,
Dan