As Books Online clearly says, shrinkfile with the emptyfile option is for data files. It is used to migrate data pages to other data files in the same filegroup.

Log records cannot be moved by anything. You need to wait until the entire active portion of the log is in the file you want to keep (use DBCC LOGINFO) and then you can simply drop the other file (via alter database or the SSMS GUI), no other commands necessary.