Today I was working on a Dynamics CRM 2016 On-Premise VM (hosted in Azure of course!) that I had configured to test something. I was restoring multiple Organizations to the CRM instance, but I came across an error I'd never seen before.
To create a new organization, the wizard must remove the current organization [OrgName]. After the wizard completes you will no longer have access to this organization?
So if I clicked yes, it did indeed import my 2nd organization but the original one disappeared. Turns out when I installed CRM 2016 I accidentally used the Workgroup product key. Dynamics CRM Workgroup edition is limited to 1 organization only. I changed the product key to the Server edition and everything returned to how I expected it to work.
I didn't find much in the way of internet search results for this, hope this helps someone in the future.