MySQL LOAD DATA IN FILE update a single column

That is because REPLACE mode deletes the records firslty.

Agree with Girish Rao about the using temp table. Here it is an example of this solution - http://forums.mysql.com/read.php?10,362103,362423#msg-362423

Also, you can use Data Import tool (Append/Update mode) in dbForge Studio for MySQL (data import from the CSV-file has no limitations in free Express Edition).