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We've experienced this quite a bit. The only solutions that we've found are to output to a new excel file, then create the pivot tables within that new file and make no changes to that file ever after that. This solution is extremely fragile and we save as a new file whenever we need to do more work after that, but it can withstand the automatic data refresh if you don't touch the file for any other purpose. The other solution is to save the file separately from the file containing the pivot tables, then copy the data into the file containing the pivot tables. This is a significant challenge when using Alteryx and definitely needs some work.
Pivot tables in Excel is simply references to another data set. Alteryx does not have the ability to CREATE/MODIFY a pivot table as that's an Excel function. I'm not sure how your Alteryx Workflow is configured or what your Excel workbook looks like, so this is primarily assumptions...
Review your Output tools configuration
Make sure it's configured to "Overwrite Sheet (Drop)" so that it does not alter any other worksheet other than the one that contains the data referred to by the pivot table
If your pivot table and data are contained on the same sheet, I'd suggest putting one on another sheet
it is possible to tell Alteryx to output to a specific range if for some reason you need to keep the pivot table and data in the same sheet, but it does add a little more complexity... there are posts/KB articles that explain how to do this if interested
As mentioned, Alteryx can't manipulate your pivot tables, but it can update the data range it's looking at. As such, when Alteryx updates the data source, you will still need to open the Excel file and update the pivot table data as you normally would.
Hope this helps, but if you have any screenshots or able to share any files that we can run to replicate your issue, that'd be helpful to provide you a better solution.
I am experiencing the same problem. Output to an existing Excel file. The old pivot table is in another worksheet, unrelated. After output, the pivot table breaks (similar to "paste as value"). All formula pointing to the pivot generate errors.
The output file opens with an "unreadable content" warning. I have to select "yes" to proceed when Excel asks to repair.