Data Refresh Confusion - Data Source Updated but Data Imported Not

So my usual data feed is endpoints on a server that query the database, and Power BI consumes the endpoints.

I do most data manipulation on the endpoints, so Power BI can receive the cleanest data possible. 

But whenever I update the endpoints for an existing report (say adding a few columns) and refresh the report on Power BI desktop, the data never gets updated. If I do "Get data" from the same endpoint, the new query gives me the updated data.

Initially I thought it was because of old cache, but after I clean the cache, things are still the same. 

I'm not sure if it's this way by design, or am I missing something here.

What I hope now is for the existing queries to update after the endpoints are updated, so I don't have to create visuals from the new query and delete the old ones. 

Appreciate any help.