For your orders missing their weights, were the weights entered manually, or were they saved in the product details?
I have experienced losing entered weights when I try to apply a preset to multiple orders, but it usually only affects products without any saved weights/dims in the products tab.
For example: if I had a list of hats that I knew weighed 8 oz but were new products without saved dims/weight, I would mass apply the weights with the side bar options. Then I would apply a First Class Package preset to these orders, which resulted in losing the entered weights and starting over. I know now to apply First Class presets before adding weights as a work around.