Case Management Studio - Can we have more than one instances in the same environment?

Previously I was working on a project to customize Case Management Studio for Use Case 1. 3 months later, that project is on hold and I now want to use CMS for a completely different use case. I realize that I can create a new case category to handle the new use case and mark the previous one as inactive. However, I have made some changes to the Base module as well and want to make sure that doesn't create any problems in the future. I have also configured data fields in the "All Cases" data section that I can view in my new case category (Which is not ideal, since it does not apply to the new use case)

What would be my best options to make sure I have a clean slate for the new use case -

1. Is it recommended to clone an instance/app of CMS using npm apn-app-manager? 

2. Should I continue working in the same instance with a new case category

Appreciate your advice on this!