In Mapping from Ethnologue 14 to ISO 639-2 I wrote about mapping Ethno 14 codes to ISO 639-2. At this time I didn't know that there actually is a mapping to ISO 639-3 provided by Ethnologue under http://www.ethnologue.com/codes/updating_codes.asp.

The SQL table create commands are given on the page, load the data using:

LOAD DATA LOCAL INFILE 'Retired_Codes.tab' INTO TABLE Retired_Codes
CHARACTER SET latin1 FIELDS TERMINATED BY '\t'
LINES TERMINATED BY '\r\n' IGNORE 1 LINES;

LOAD DATA LOCAL INFILE 'Update_Mappings.tab' INTO TABLE Update_Mappings
CHARACTER SET latin1 FIELDS TERMINATED BY '\t'
LINES TERMINATED BY '\r\n' IGNORE 1 LINES;

The page does some step to step description how to upgrade, so I guess there's nothing more to say here.

Update:
Table Update_Mappings has three mappings where the given code doesn't exist in ISO 639-3:

mysql> SELECT * FROM Update_Mappings WHERE New_Code NOT IN
(SELECT Id FROM ISO_639_3 UNION SELECT Id FROM ISO_639_3_Retirements);
+----------+----------+-------------+
| Old_Code | New_Code | Name        |
+----------+----------+-------------+
| DLC      | dlc      | Dalecarlian |
| JMK      | jmk      | Jamtska     |
| SCY      | scy      | Scanian     |
+----------+----------+-------------+

Further more it has 102 mappings to codes that at the time of writing are retired:

SELECT COUNT(*) FROM Update_Mappings WHERE New_Code IN
(SELECT Id FROM ISO_639_3_Retirements);