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Hi there. The most common reason for this is a skin disease called 'dermatophytosis' otherwise known as ringworm-a fungal skin disease. It is more common over winter months when small mammals are getting less sunlight, just because this slightly suppresses their immune systems. It causes bald patches, which can sometimes be slightly scaly in appearance. Other external parasites are very rare in Chinchilla's due to the dense coat.
There are several ways to treat this- but all treatments are prescription only from the vet. You can either use a lotion called 'Surolan' which contains an antifungal(or other similar antifungal lotions), or there are oral ringworm medications available- speak to your vet about which one they usually use for small mammals.
Hope this helps