I had the same problem where the sales stages of opportunities disappeared after upgrading to CRM 2016.
I deactiviated the opportunity business process and reactivated it. The stages came back.
The only problem now is that for the opportunities that were already there before when I try to change the sales stage an error message comes up saying:
The requested record was not found or you do not have sufficient permissions to view it. If you contact support, please provide the technical details.
I am however a system administrator although not the person who installed CRM. I cannot move to a new sales stage in opportunities and when I try to delete the opportunity the same message comes up.
When I create a NEW opportunity however, after the deactivation and reactivation of the business process, there is no problem moving the sales stage on these new opportunities or deleting them. It is just on the old ones that I can neither delete them or move the sales stages. I can close them and do other things though like change dates etc...
Puzzle... Any ideas?