When I had to compare text files at a previous company, we'd use Beyond Compare to show only the lines that differed. It was smart enough to also skip empty lines so that the line number did not matter. It was really useful when trying to compare code. I haven't come across an clean way to do this in Alteryx.
My first thought was to join, but then I had an issue where one file had a replicated line in it and the join did not catch it since it would join with the first occurrence of the other file.
Any suggestions on this?