Are the calculated fields actually within the published data extract OR are (were in the case were they're invalid) they only in the workbook?
A good way to find out would be to connect an empty workbook to the data source and see if the calculated fields are there.
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Ok, I understand now and can only make assumptions as to what it looks like is happening. It appears you're trying to link to a calculated field within a secondary data source. Logically this would create problems as an extract is a stand-alone object, it appears it's not possible to build in dependencies on other extracts that may or may not be available for the extract to read.
I think you would be better having cross extract calculated fields within a workbook where the extracts are actually available, which does mean they wouldn't be available in a published extract. If they have to be available within a published extract then based on what I'm seeing the data from the different extracts would require combining into one master extract.
Perhaps someone else has a better idea than I about this.
I think I've seen this issue before. Try publishing the secondary data sources (orange check marks) first. Then republish the primary data source (blue check mark, has these broken calculations). When you publish the primary data source, you may get a warning message, but just hit okay. Then connect your workbook and swap in these new, published data sources. The calculations should be working now.
I extract the datasource and deleted the fields with problem after I created the calculations in workbook.
Thans very much!