As per the HL7 specification, QIE defaults all outbound HL7 messages to CR only ('\r'). This means that no matter which line endings are used on the incoming message, the outbound message will be changed to use CR only. However, you can change the line endings that will be used on the outbound message by using the Code Wizard function,
message.setHL7EndOfLine('eol').
This allows you to specify exactly which line endings you would like to use on the outbound channel.
To add CR/LF to the end of each segment use the following code:
message.setHL7EndOfLine('\r\n');