I'm sure you understand what you're doing, but you have not explained it clearly enough for anyone to help you. For example, this
get alwys in the output one complete line and the different input lines are separated by X'3D.
makes no sense -- iconv function does not convert lines, it converts characters. For any real help, you need to provide a sample input string, the iconv output for that string (use the Code tag and hexadecimal display so we can see exactly what each character is), and then tell us where you think the problem is and why you think it is a problem.
The EBCDIC hex value for a carriage return is X'0D' while a newline character is X'15'. Either -- or both -- of these could be used to mark lines, although iconv does not pay attention to line ending characters since it is based on the buffer length passed to it.