I would put the '\n' (yes, exact symbol is critical, as always in code!) when logging the data itself and NOT in the file copy program. For one thing, how would the file copy program know when a line is ended? Usually by a character which is usually '\n' (10) or '\r' (13). The time to put it in is when the lines are made.
If you want to trot out the data logging code then we can look at that and maybe discuss why it is not part of the code that runs on the "send" Arduino... because I am getting the feeling that a third Arduino is involved/wasted.