Separate SSL Certificates for Web Application and API

Question

I have a data collection / reporting web application hosted on an AWS Lightsail instance with Ubuntu 18.04 OS and Apache2. I use a 'Lets Encrypt' SSL certificate on the site. This all works fine.

I also have an embedded device which uploads data to the website via an API. The embedded device is currently not operating on SSL, but I need to change this. The embedded device can communicate on SSL but its not easily updateable in the field. My concern is that the CA certificate that is embedded into the device cannot be updated, and so using the same 'Lets Encrypt' certificate, means that a change in the Lets encrypt certificate will render the remote embedded device unable to connect to the server.

The common solution to this problem is a self signed certificate over which I have total control, and yes this would fix the problem, but it would create another problem. If I use a self signed certificate, then any user connecting to the site to view data from their PC would get an Untrusted Certificate warning on their browser, which is not acceptable.

So, to fix this ideally I would have my web app protected by 'Lets Encrypt', but the API protected by a separate self signed certificate. However, both web app and API need to be on the same domain. Also they should ideally also both be on the same standard 443 https port.

Is there a way to setup the web app and API to serve different SSL certificates?