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.CER certificates can be used during the migration of Azure Cloud Services to Extended Support in the following ways:

1. Secure Communication: .CER certificates are used to provide secure communication between the Cloud Service and the users. During migration, the existing certificates can be reused, or new ones can be generated and installed to ensure secure communication.

2. SSL/TLS Traffic: Cloud Services use SSL/TLS traffic, which ensures secure communication over the internet. .CER certificates can be used to authenticate the server, providing a secure connection during migration.

3. Authentication: .CER certificates can also be used to authenticate users during the migration process. This can be useful while accessing the database or any resource across different domains or networks.

4. Encryption: .CER certificates can also be used to encrypt the data that is being transmitted between the Cloud Service and the users. This ensures that sensitive data is not intercepted or accessed by unauthorized users during migration.

5. Code Signing: During migration, code signing is necessary to ensure that the code is authentic and has not been tampered with. .CER certificates can be used for code signing, which ensures that the code being migrated is authentic and secure.