Hi there.  Lilies are susceptible to two different Botrytis species.  Botrytis elliptica and Botrytis cinerea.  I have included some photos found on the internet showing botrytis on lilies flowers, buds, leaves and the stems.  It sounds like you have already begun to fight this disease by digging up your bulbs and replanting them. 

Botrytis is a fungal disease which overwinters on the dead plant debris.  In the Spring new fungal spores in or on the soil ripen and infect the new shoots as they emerge.  Infection is most likely in wet foggy weather when temperatures range from 50-65 degrees over a period of several hours.  In other words the Willamette Valley’s weather is perfect for its growth. There are several things you can do to reduce disease pressure in your beds.

The first is to remove all plant debris at season’s end. Pull the lily shoots up as soon as they can be easily separated from the bulbs.  Removing infected flower buds also helps control the disease.  Annual digging as you did also helps.  You should also reduce the density in which you plant your bulbs.  Increasing the distance between bulbs allows maximum air circulation around the plants as they emerge.  Finally rotate planting sites every year.

If you continue to have issues you need to take a sample in to the Extension office during the growing season and have the Master Gardeners on the desk verify it as Botrytis.  At that time the Master Gardeners on the information desk can provide additional recommendations that can help you rid your lilies of this disease.