I would do this way :
1 ) Write a Stored Procedure to do the update with commits each bunch. This will continue till all rows are up-to-date.
2) Write an update job that will be tied to daily update job. This update will be in comfortable bunches.
If the situation is such that existing update job cannot be modifiled to include everything, then this data can be staged somewhere and the missing columns can be filled in staging. This make sense only if final data has to be complete before real update and that you do not involve this production database in staging operation.
In other situation, you are better off with stored procedure, same as in step 1) above. Also the stored procedure can be customized to include both 1) and 2).
It does not seem practical ( as much I understood from your explanation of need ) to run update job from CLP or OS because the daily update is doing this daily; you need another job to supplement these columns which seems safer with stored procedure.
In any case you are costing the update double.
Hope this helps
DBFinder