Hello Shubham Raut
unfortunately, it is not possible to remove the EnableMongo16MBDocumentSupport capability from an existing Azure Cosmos DB for MongoDB account. This capability cannot be disabled or removed, as it is a required feature for enabling 16MB document support.
If you need to enable CMK encryption, you will have to create a new account without this capability.**
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Regarding the data migration, ADF is the best option and please refer the below document for more steps.
https://learn.microsoft.com/en-us/azure/data-factory/connector-mongodb?tabs=data-factory