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I figured out my problem. The problem was occurring due to varying delimiters in the data. The first two rows of the csv are a header that is pipe "|" delimited and the body was semicolon ; delimited. By configuring the input tool of the macro to use the carrot ^ as the delimiter (just a random symbol that should never show up in the data) the input tool was able to read in the data as one column. Then the sample tool was applied to skip the first two rows. This is the output of the batch macro. The text was then split to columns using the ; delimiter and all is well!
I have attached a sample data to show what it looked like!