I ran into this problem today and wanted to document how I resolved it.
I had workbook A connected to extract X.
I then created workbook B and also connect it to extract X.
Then, as I messed with calculations and otherwise worked on workbook B, refreshing the extract from both workbooks A and B caused problems.
I needed to make an original copy of extract X' connected to workbook A.
I also needed to leave the more recent extract X (with my new calculations) to workbook B (this is the easy part).
If there's a better way, please advise. If I did not do this, I would otherwise connect to the extract as a non-extracted data source and would have to extract it again from within a workbook if I wanted to optimize and do other things.
This approach assumes you have your Tableau files in a server folder that backs them up such that previous versions are available.
Otherwise, for steps 1 and 3, try to find a version of workbook A from before you screwed with the extract in workbook B.
Here's what I did:
1. Right click on workbook A and select "Properties."
2. Click on the "Previous Versions" tab and select a previous version to use.
3. Select "Copy" and copy the file to your desktop (or a different folder from which it is located).
4. Package (right click...) then unpackage this version of workbook A.
5. Find the extract stored in the unpackaged workbook folder that appears after unpackaging it.
6. Cut and paste it to your desktop and rename it to fit workbook A.
7. At this point, it would be convenient to delete the folder associated with the unpackaged workbook A, packaged workbook A, and the original workbook A (if not, then change the name of the original workbook A).
8. Open unpackaged workbook A.
9. The "extract not found" error should come up. Select "Locate the extract" and connect to the extract (X') from the unpackaged folder (now on your desktop).
10. Make sure things in workbook A are honky dory and save.
11. Rename the extract in workbook A (right click on the extract name in the workbook at the top of the data window on the left).
12. Put everything back in the correct folder. This may require re-saving to ensure the extract path is correct.
12. Refresh extracts in workbooks A and B to resolve any errors, then publish workbooks again to server if needed (to ensure that scheduled extract refreshes, if existing, will not negatively impact the published workbooks).