Thanks for reaching here! Yes, the presence of the certificates in the Function Apps may be due to propagation since they share a resource group with the App Services. The certificates in the Function Apps are inactive due to no explicit bindings, making only the two App Services the real users of these certificates.
A certificate uploaded into an app is stored in a deployment unit that is bound to the app service plan's resource group and region combination (internally called a webspace). This makes the certificate accessible to other apps in the same resource group and region combination.
If you are using cert store( key vault ) to store you ssl certificates then you need to pass the key vault certificate uri as application setting to the functions app.
You can store the public cert under the function app TTL/SSL settings & refer this documentation for accessing the certificate in your application code.
Regarding your second question, if the primary certificate used for the App Services expires, Azure will not automatically bind and use the other available certificate. You will need to manually set this binding. If you do not take any action post-expiration, your App Services will be rendered inaccessible.
To avoid this situation, it is recommended that you set up a certificate renewal process to ensure that your certificates are always up to date
You may refer to below document link would be helpful.
- How can I automate adding a bring-your-owncertificate to an app?
- Frequently asked questions for App Service certificates
Let us know if further query.