@Chandrahasan Subbaiyan Welcome to Microsoft Q&A Forums.
You should first regenerate the key which is not currently being used by the application configuration.
This process could take a few hours depending on the size of your database because the key is used to encrypt the data at rest.
You can have separate pipelines for regenerating the keys and updating the configuration so you can run the latter over the weekends or during non-business hours.
Azure CosmosDB now supports Data plane role-based access control (RBAC).
So, you can disable the primary/secondary keys on your account and do away with the need to rotate keys completely.
Here is a tutorial that demonstrates the rotation for Azure Storage Account, but you get the idea for Cosmos DB as well.
Automate the rotation of a secret for resources that have two sets of authentication credentials
Please let us know if you have further questions.
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