Firstly, there will always be losses with seedlings. Don't beat yourself up when this happens. But certainly, we can always attempt to minimize casualties.
40F nights and 50-55F days isn't cold enough. That would be normal spring temps, and I'm not too surprised that it's not inducing dormancy. In fact those temps are pretty ideal for building healthy "bones" in most plants. Warm enough for very significant photosynthesis (energy production) and storing sugars, and cool enough to curtail respiration (the chemical reaction that uses up sugars.). So, at least on the plus side, I'll bet your babies have been storing up a lot of food in their bulbs.
you could grow them on under lights, thereby getting the most growth and larger plants in the end. But I see no reason why you shouldn't be placing them where temps get down to freezing, and after a week or two: where temps stay at or below freezing (but above mid 20s). You'll be surprised how resilient even seedlings can be. All lilies, even seedlings, have a natural antifreeze in bulbs and roots that prevent them from actual freezing, even if the soil ball is frozen rock hard.
