I need a bit more information. I presume you mean that the shallots you did not harvest put up new shoots this spring. How big were the new shoots when you separated the shallots?

Yes, the shoots that came up this spring. Here are three pictures. I had one more that I pulled up yesterday to take the picture. They are growing in the same raised bed that I pulled them from. On the left of the picture, I have five Asparagus plants growing. To the right of the shallots, I have about a dozen bush snap pea plants growing. They are three feet away from the closest shallot. Some of the peas are just starting to show flowers. The several shallots plants that I dug up all originally looked like the picture of the ones I pulled up yesterday. I pulled the shallots apart and planted them about three weeks ago. These beds are three years old. I put some compost in the garden bed when I planted the shallot starts. One of the starts looks like it's going to seed. It's in the middle of the third picture.

Usually it is best to divide and plant the bulbs in fall or in the spring before leaves emerge. Shallots are typically harvested in the fall when leaves begin to die, just like onions. The bulbs are pulled from the ground, divided, and allowed to dry down for a few weeks before replanting in the fall or the next spring.
In your case, you are attempting to transplant growing shallots, and given the very warm and dry weather we have been getting, it puts the shallots under a lot of stress and it looks like the leaves are dying. They may eventually recover when the shallot is able to re-root. Just keep the soil well irrigated until they establish and new undamaged leaves begin to emerge. There is a possibility that the stress of this has pushed the shallot into making seed, but that is not all that common normally, so i doubt that many of them will produce seeds.