There is no need to dig them up. Just clip off the stalk below the seed heads leaving most of the stalk and leaves on the plants to allow them to feed the bulbs for next season's bloom. Once the leaves and stalk turn brown, you can clip them off at the base.

Ok unconventional solution. Try it or not.. Continue to remove the affected leaves and make sure there is plenty of air circulation around the base of your plants by removing lower leaves and limbs and weeds. I thought the rain was great till, my zucchini and tomatoes started an early mold/ blight..... yellowing of leaves and dying.. But I found a dirty little secret no one wants us to find out about.. Someone in South America discovered spraying milk on your zucchini, cucumbers, melons and tomatoes prevented, mold, milky spore and tomato blight. The study I read suggested a 10-30% mixture of milk to water was optimal... 1 part milk to 9 parts water in a spray bottle works fine. With all the rain we have been having you may have to reapply but is sure is alot safer and cheaper than fungicides. It seems the natural bacteria in milk somehow combats the mold and blight in addition to building the plants immunity by absorption through the leaves. According to the study I read, this milk solution was 90% effective and a whole lot cheaper than traditional copper, fungicide etc. According to a New Zealand study on the same solution they found that skim milk was just as effective as whole milk and as a result of the lower fat content also reduced the possibility of an odor problem. It seems to be working well so far for me... let me know if anyone else has any luck with this...

I cut them back the 1st year when the hot weather hit just before the monsoons. I was going to pull them when I read a tomato column by a local "garden Expert" who said that was the thing to do. He suggested cutting them back about a half until the plant started putting out suckers and then trim them back to about 1/3 when the suckers were about 6" tall. Last year was a light monsoon season so I was watering almost every day in the evening and they just kept growing. When it started cooling off in the night in Sept then they started blossoming and set very well. I wrapped a bit of plastic around the plants using t posts and had tomatoes until Christmas. If it was a fluke the it was one that my family and I enjoyed. If you have the room, give it a try, you have little to lose and more to gain.

Your soil looks fine in that photo.......lots of perlite and can't really overwater it. When you water try not to wet the actual crown/leaves of the plant (just the soil/roots), and water on the morning of a bright day. These are both more applicable in winter. Your biggest problem growing that plant was lack of light. Unfortunately those etiolated/stretched leaves will not heal or turn normal. Assuming the crown is healthy, and growing conditions remain good, it will eventually produce another normal pup or two. Keep it under good growing conditions. You may just want to buy a new plant and grow in the better conditions you are providing now.