If your baby was able to nurse substantially when she was ill, then I reckon it's not a supply problem -- I think maybe your breasts became more receptive to baby's suckling and are not as responsive to pumping as before.
More nursing/pumping results in a greater milk supply. If you consistently reduce the amount of time nursing or pumping for several days, your overall milk supply will decrease and you can expect to see a decrease during pumping. Keep pumping and nursing the next couple of days and see if the output increases.
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