Thank you for contacting the UVM Master Gardener Helpline with your question about your shallots. How disappointing to see your harvest under attack.

One of the helpline experts suggested that you pull one or two of the effected shallots and look at the bulb/root for evidence of root maggots. This article entitled “Cabbage and Onion Maggots” published by the University of Maryland Extension includes a picture of a damaged onion. https://extension.umn.edu/yard-and-garden-insects/root-maggots

Utah State University Extension published “Root Maggots” which includes pictures of infected bulbs and a picture of the mature fly and includes information about how to control them: https://extension.usu.edu/vegetableguide/onion/maggots

Another article you might find useful is “How to Grow Shallots in your Garden” published by Utah State University Extension: https://extension.usu.edu/yardandgarden/research/shallots-in-the-garden. This article lists some problems you might experience with your shallots and how to treat them.

You can also check out this article entitled “Garlic Bulb Mites” published by the University of Maryland Extension which mentions the leaves turning yellow: https://extension.umd.edu/resource/garlic-bulb-mites/

If this information does not address the problem with your shallots, you can send in pictures of the bulb that is impacted, close-ups of the leaves, in particular the area between the bulb and start of leaves, and any obvious damage to the leaves.

If you have any additional questions, please feel free to reach out.