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Lime is really only for small quantities.
The pits have already flooded, so the environment has lots of faeces spread around. Spread it on the fields as it is, but do not grow salad or other crops that do not need cooking. Educate farmers about the need to wash the produce and wash their hands after working in the fields. The ground is contaminated anyway so this would have to happen whatever you do with the sludge. An improvement would be to bury it or plough it in.
But - do the latrines need to be emptied? check to see if the water is receding. Are the pits full of faeces or silt? Would it be more sustainable to cap these latrines and build some that are more resilient?
Is this flooding frequent?