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I'd built a process not using Alteryx on files delivered from an e-mail scheduled report. I used powershell to extract the datasheet, save as a CSV and then ingest like normal.
When I switched to Alteryx I had the same issue here as something is off with the excel files... From what I can finally deciper, the generated excel files are missing their <?xml declarations, which by opening in excel and re-saving it effectively fixes the formatting to be "correct" and what Alteryx expects. I've battled trying to wire up a powershell script to automate the open and save, but I don't know that's going to be compatible on our server.
On a hunch, I thought about trying these files as .xls or Legacy xlsx... and so far it's worked!
Use input data tool
Select excel file
Get the sheet selection dialog box
Select "cancel" as it can't read any sheets
change Input tool "File Format" to "Microsoft Excel 1997-2003 (*xls)" or "Microsoft Excel Legacy (*.xlsx)"
I now get an error that I must select a data sheet
Re-try selecting the "Table or Query" in the tool settings.