Today I ran into the very same problem. I have a data source to a file in SharePoint Online. The file was moved to a different location in SharePoint. I updated the path in Power BI Desktop accordingly, then published the PBIX file to the Power BI Service.
Now the data refresh in the Power BI Service doesn't work anymore, because the data source is duplicated: both the previous version and the new version show up. And the old one obviously doesn't work anymore.
This makes the refresh impossible. There is an extra - and broken - data source in the web, which doesn't exist on the desktop app. I deleted the data set, then re-published it: that didn't change anything. There is a ghost datasource, which is visible only in the web service.
I saw in this thread that this was supposed to be fixed a year ago. Well, it isn't. Or it came back. Anyways, it needs fixing. I can reproduce the issue.