I would hazard a guess and blame it on the fact that you only seem to be watering near the main stem and not the whole pot. This may have "signalled" your plant, over time, that water is scarce and as an adaptation she has reduced the size of her leaves to cope with the possible low moisture content of the substrate. Mind you this is just a guess on my behalf and I do not hold a degree in plant psychology!
You really should be watering the entire pot, roots will not grow and explore into dry areas. As you seem to be growing in coir, there is very little chance of over watering, just don't water too often and everything should be fine. A good deep watering, to run off, every few days, is far better than giving small amounts often, Just remember to wait until the top 1-2 inches are dry before watering again and water from edge to edge of the pot. Watering to run off will also help prevent excess nutrient salts from building up to toxic levels and also ensure water is getting right to the bottom of the pot, which is where most of the roots will be by now.
This leaf mutation has nothing to do with cotyledon damage, big or small.
Sometimes plants with broad leaves will revert to growing narrow leaves when flowering, so this could be perfectly normal too, but watering properly and deeply is vital for strong and healthy growth.
Hope this helps,..........
Organoman.