Can we remove our Custom SSL/TLS certificate and switch to the TLS certificate provided by Upsun?

Yes. Upsun issues free Let's Encrypt TLS certificates that are renewed automatically every 90 days. 

Retrieve the list of certificates with:

upsun certificate:list

From that list, get the CERTIFICATE_ID of the certificate you want to delete.

You can remove your custom certificate with the following command:

upsun certificate:delete <CERTIFICATE_ID>

You can then redeploy and the Let's Encrypt TLS certificate will be automatically applied.

For more information on this feature, please see the TLS Certificates section in the Upsun documentation.