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Discoverer creates files for a windows environment which should just have the LF to separate a line. Unix files have LF and CR as line separators. You could try using a Discoverer calculated item to append the CR to the line using for example col1||CHR(13) but this would not be a very satisfactory solution.
However, there are numerous tools that you can use to convert windows files to unix files. I am not sure what you have available in your environment, but I would explore this option first.
I don't think the customer would be up for that suggestion (although I like it), but you mentioned something that made me think of another option... I decided to change things on my end and swith the SSIS package to Unicode encoding and adjusted the Row delimiter to LF only. That way, all the customer has to do is change the file encoding.
Thanks again - I appreciate your help with this!