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I had the same error, but I saved my query anyway while I went to search for the solution. When i came back to resolve the line breaks (having read your post), Alteryx sorted it out itself. I guess what happened was, when I closed the input tool having pasted my query into the SQL editor, Alteryx removed any formatting of the query (it all gets displayed as one line anyway). But the error message persisted nevertheless, until I went back into the 'edit query' mode, when I found that the SQL I pasted was now all displayed as one long string. I didn't change a thing, just clicked apply settings, and the error disappeared. It could have been designed better.