DSXchange

What DB are you using? theres is something like 'Transaction Handling' and this can be enabled by checking the option: 'Enable Transaction Handling'.

may be you can use that or if you don't want to design in that manner go for 2 jobs. UPDATE in the first job and in the second job INSERT.

Yes, I have seen this problem many times. You need the benefit of a non-caching, instantly committed transaction without the performance overhead associated with such activity. If you look at the SCD question posted just a few days ago, where I listed a numerous number of links to posts covering this topic, I describe at length the problems with designs exactly as yours.

DataStage Server has hash file technology that allows you to do all of your such work off-target, meaning in a sandbox setup within hash file structures. You'll find that DataStage has high-performance reference and write capabilities to hash files, without all that messing database overhead. Even with read/write caching disabled, you'll find that performance is very good. Couple that with multiple clones (instances) of a job tackling source data in a divide-n-conquer approach, you'll get thru your datasets quickly. Then, you can separate inserts and updates into distinct load files and then bulk load your inserts and then do updates.