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When running a workflow to append data to an existing Excel file, Alteryx creates 2 .bak files and the original .xlsx file disappeared. When running the workflow the second time, one of the xlsx.bak files turns into an .xlsx. When running the workflow a 3rd time, it turned into 2 xlsx.bak files again. It may happen whenever updating a pre-existing file.
The issue is user-specific. When you press F5 to refresh the Folder, one of the .xlsx.bak is replaced with an Excel file .xlsx. The issue is not related to Alteryx, but to Windows. The problem is that the Folder is not refreshing automatically in Windows.