Workbooks 'sharing' a data model

[Jaffa]

Here is the situation. I have created a powerpivot workbook and saved it on OneDrive and it refreshes fine on Power BI. I create a copy of it, amend some of the queries (changing where clauses but not changing anything else) and save it on OneDrive. When I bring it in to Power BI, I don't have to reenter the connection login becuase it uses the same one as workbook 1. When I refresh it, it pulls the workbook 1 data in. It is as if the model from workbook 1 is cached in some way and the two work books share it. 

When I changed the way two tables were linked and in doing that removed the original column it gave me an error when refreshing about the column not existing.

My question is how do I differentiate the two so that they refresh separately? I cannot realistically create the reports from scratch which might possibly give a different connection identifier as I have a number of them to do (they are individual reports for salespeople). And is this expected behaviour? I got the same result when using power query as when just using powerpivot connections.

[Jaffa]

Having thought about this further, I think this may actually be an occurrence of this problem:

http://lmillott.azurewebsites.net/?p=171

They are not sharing a dataset, it is just that the changes to the query are not being reflected as Power BI is looking in the wrong place. Unfortunately the solution outlined in that post no longer works in 2016 as the queries are not in that connection file.. Any ideas?