Re-enable Prompt: You are making changes to your Certificate Trust Settings during .pkg installation

This may seem like a silly post but I thought I would ask.

We have a particular piece of software that is being used in conjunction with a third party scanner that has an installer which needs to apply an additional security certificate for the scanner's app suite to run. When running the installer on the original machine, the user accidentally selected Cancel when prompted, and we are unable to get the prompt to show with subsequent retries of installing the application. It may be worth noting as well that the installer uses Mono for post-installation scripts. However, when installed on a separate Mac, the settings were updated, the prompt was accepted, and everything is functioning normally.

Short of a major support case, would there be a quick fix for this such as removing or altering a PLIST file to get the security prompt show on the original Mac?