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encrypt schema documentation for automatic field-level encryption:
encrypt cannot be specified within any subschema of the
additionalItems keywords. Specifically, automatic client-side field level encryption does not support encrypting individual elements of an array.
If you currently have an array mixing values that need to be encrypted with those that do not, I recommend separating the values into two arrays in your data model so you can use automatic field-level encryption.
An alternative approach would be to use Explicit (Manual) Client-Side Field Level Encryption, but this would require modifying your application code to include encryption/decryption logic in relevant read & write operations.