Great progress! Keep up the great work and build habits for the rest of your life.
This seems like a good idea to me, even if not done all the time. Personally, I tend to periodically take a week to measure everything and calculate macros, then figure out if I need to adjust. I don't do that all the time, but it gives me a pretty good idea of what is going on with a plan that is specified otherwise. That is, I can easily get an idea of if I need to decrease my carbs and how much, like by a cup of rice a day, half a cup a day, or what? Or what certain replacements would do, like switching chicken breasts for chicken thighs.
I was thinking the same. I have always done better when losing weight keeping in some animal fats and keeping carbs lower (generally 50-100 g/day). Besides the yolks having fats that your body needs, they also contain a ton of micronutrients. If you can get a calculation of the macros in that meal plan, you might be able to see if you can cut some of the nightly carb sources or the milk or something. So, I think what I would recommend is that you take the few minutes to get a rough macro nutrient and caloric breakdown for those meals and days. If you post that you might be able to get some particular feedback there, and in any case you could then readily see what adding back the yolks would do, or changing one of those chicken breasts to a few thighs, or whatever. In any case, that is just something to consider.