This problem would come up with some of my species lilies from time to time in my earlier years as I learned how to grow them. At that time, the garden was rich clay, exactly what lilies (especially species lilies) hate, and many lily experts were surprised I could get them to grow at all. The secret was that the clay was never water logged, except in early spring when species lilies have greater tolerance to excess moisture. This was because the garden was bordered with lilacs and a huge Norway maple that sucked up water like sponges. Even after the occasional summer downpours, the clay was wet only briefly before the lilacs and maple mopped up the excess water. The other "secret" was that the soil was never cultivated, except to plant the bulbs themselves. (Due to the complicated regime of soil physics and soil flora involved, you'll just have to believe me, here.)
But then something started happening: climate change. I could no longer depend on seasonal ranges of norms. The occasional downpours could turn into torrents, and my natural "sponges" were beyond capacity. I had not changed my growing method to fit the new weather regime.
As Lorn says, my infections originated at or just above the soil line, and would manifest themselves just when soils started drying out, and just as I began to think I might have escaped the bad weather without casualties. Then I would see the symptoms, and once I had a tall stem just topple over. The bulbs were never affected by this disease, although sometimes they were consumed by an unrelated basal rot.
But we shouldn't confuse this with the normal phenomenon of natural senescence: when a lily stem may die back in late summer or fall. When this happens, the progression is slow, and you won't detect any evidence that the lower stem near the soil surface is different from the rest.
