My sons have XLI and keeping their ears clean has always been a problem. The skin build up and sometimes outer ear cleaning can be a challenge. Now that my boys are older it is so much easier for them to tell me that they cannot hear, or that their ears feel "stuffy" or "clogged", sometimes the teacher will report that they seem that they are not paying as much attention in class, or asking for things to be repeated. (shouting and talking louder than normal too)
I try not to let it get to that level, but keeping their ears free from build up is a challenge.
When my middle son was 2 we went through the same thing, the Dr thinking he needed tubes in his ears. We and the new DR I sought out, realized that a thin layer of Wax/dead skin particles had actually covered the drum. We did have to have that removed by an ENT and the process as I recall was slightly painful at the time. (there are numbing drops now) I am glad that we sought a second opinion, because tubes are used to drain the inner ear, from fluid thats not reabsorbed into the body and keeps regularly becoming reinfected. That WAS NOT what we had. If the boys get an infection from the ICHTHYOSIS, (not a regular illness that causes bacteria or virus to settle into the middle ear) If they get an infection from the ichthyosis, it is more like an outer ear infection, like "swimmers ear" would be. We clean and treat their ears similar to swimmers ear.
I think also talking to moms, that they see "potatoes" falling out of the ears..lol
I usually only worry when the potatoes stop falling out.
It is important however to keep their ears clean, so that proper seech can develope regardless of it being an inner ear or outer ear problem. At the time, my middle son had an underwater type speech. I guess it was natural for the first Doctor to assume that it was middle ear. His speech made huge strides and improvement once that thick layer of skin build up was removed.
It was hard for the ENT to see also by the way, it was glued so thin and firmly to the ear.
My sons speech went from not using "SSSSS" and "FFFFF" the subtle sounds, because he could not hear them. I know I have posted this eons ago on this website, but an example was that he would say "gee that duck?" He continued to say GEE for quite awhile even after the procedure because that was how he learned that word. But, he could sing his ABC'S and say "C" clear as day because he learned that after the procedure and could hear the subtle difference. I do not know if this helps, but for now I think you made the right decision.