I typically fertilize our 50+ lily's with granular bulb/bloom food just as new shoots emerge. then once again as the "eyes" appear. then a few times with diluted liquid fish fertilizer once all the flowering is done- usually until mid/late august, providing all the nutrients they need for huge bulbs and huge looms the following year.
I would have say your bulbs rotted from issues dealing with excess moisture, on some level. I live in Seattle where it rains 9 months a year and we rarely have rotting bulb problems, so im a little stumpted here.
perhaps there was something else going on as well...? we have lilys in pots that we leave outside all year long in regular potting soil, as well as having bulbs in the ground, and rarely do we not have one come back. the lily's in the pic below have been in that cedar box for several years in a row, without so much as even touching them- no rotting problems what so ever... at the time this pic was taken they had been in there for probably three years in a row. we finally dug them up this year to divide them. they were in perfect condition. sorry I wasn't much help. I just don't have much experience with rotting issue because we don't get it too bad here. perhaps someone else can lend you a little insight...