You are trying to configure the following scenario:
You have a workflow project named "workflow-A" and it uses an Application Properties "app-prop-A" (default instance).
You duplicated the project into a new workflow project named "workflow-B". The new project (workflow-B) uses the same properties but needs to use different values in the properties (Different Database string connection, other file paths, etc...). To achieve this, you created multiple instances in the "app-prop-A"; workflow-A uses "default instance" and workflow-B uses "testing instance".
However, when the application property refresh occurs, Workflow projects that are using the same properties profile but are using different instances no longer properly reference their specified instance.
We recommend the following.
1. Run only one instance at a time.
2. Placing each instance on it's own Workflow server.