see: a marker such as FFFD (REPLACEMENT CHARACTER) in http://unicode.org/faq/utf_bom.html

and see native2ascii --help
 
 -encoding encoding_name
 Specifies the name of the character encoding to be used by the conversion procedure. If this option is not present, then the
 default character encoding (as determined by the java.nio.charset.Charset.defaultCharset method) is used. The encoding_name
 string must be the name of a character encoding that is supported by the JRE. See Supported Encodings at
 http://docs.oracle.com/javase/8/docs/technotes/guides/intl/encoding.doc.html
 
a case

 $ file yourfile.properties
 yourfile.properties : ISO-8859 text, with very long lines
 $ native2ascii -encoding ISO-8859-1 yourfile.properties yourfile.properties