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What kind of tortoise? If their skin is flaking off you may be keeping them in an environment that is unsuitable humidity-wise. Tortoises which are used to arid climates, for instance, will have their skin "flake off" if they are kept in environments that are too wet. Substrate plays a big part in this.
I think I remember you posting about a Marginated Tortoise once. If this is the same tortoise then humidity could be the cause. If these tortoises are kept in moist substrates they can suffer a from a sort of scale rot -- it can be found similarly in snakes. The scales will come off in large "flakes" when this happens.
If this is the case, you can remedy it by changing the substrate to something drier such as newspaper. I would also recommend applying a good antiseptic to the affected areas.
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