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I got to resolve the issue after placing the required folders in both primary & worker node of alteryx server. Whenever my workflow was running on worker node, it was failing because worker node was not having required folders which I had placed on primary node.
So if your server is configured with both primary nodes & worker nodes, it is necessary that settings you do on primary node are also performed on worker nodes.
It was a great learning. Thank you everyone for coming out with suggestions.
UPDATE: I have found another Alteryx Salesforce Input tool here: https://gallery.alteryx.com/#!districts/5273c98b20aaf90e787e4319 that appears to use QueryAll and will select deleted records. It is probably easier to use instead of copying the existing Alteryx Input Tool and editing it. The only downside is that I think it uses the Label and not the Name for the Salesforce Object.