Not all that sure about that,
When you get a married extension the paperwork isn't enough, they want to see her at immigration and in the home (and they generally ask her if she's happy in the marriage). As far as I can see the same rules will apply to a dependents extension, dependent will need to be present in the home, and they will ask him if he's happy living with dad.
But I could be totally wrong, so OP should call immigration and ask if his dependent extension is still valid when his dependent son has run away from home. That would be better than immigration finding out later and ruling him as being on overstay since the boy moved out.