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I am frequently running into the same issue. Here are the steps I am taking:
To resolve the issue, I do a refresh in Power BI Desktop and re-publish the dataset. Power BI service refresh then works again. Note that I'm not changing any of my queries or anything else -- I simply click the Refresh button.
Surely this is a bug -- I can't see how this is by design.
Important note: I am not applying any transformations to the removed column in Power Query Editor inside Power BI Desktop.
P. S. There should be a separate label for dataflows.
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