ISSUE:

We have two engines in one deployment and wanted to run one engine in http and other in https.

Solution:

It is not possible to have different configuration for the single deployment. Configuration is tied to each deployments and what ever change we do ,it will be done for all the available engines on that deployments.

We normally use multiple engines as part of single deployment when the purpose is to keep same configuration across all data collector.
 
In this case, we can  create separate deployment for both the engines.