From the point of view of FTP, Cobol COMP-3 data is binary data. If the data set is sent as a text file, the FTP on the sending side translates the data to its understanding of ASCII, and the FTP on the receiving side translates the data from its understanding of ASCII to EBCDIC. The translation of non-text data (e.g., binary data) is not well defined, even within my comments about "understanding ASCII." In addition, attempting to send non-text data as text data may cause the transmission to fail in unpredictable ways.
If the data is in fixed length records, send it as "binary" data so nobody translates anything.