Good point. While some South Korean factory jobs may get lost to North in the earlier years of Korean reunification, it will eventually boost up Korean factories' global competitiveness, especially so in developing world like India and Latin America where cheaper goods are more desirable, and then bringing greater good to the United Korean economy in the long run.South Korea is primarily an export driven economy. For example, they have set up large factories in India (Hyundai cars, Samsung phones, LG air-conditioners etc) and captured good market-share in India. Much more than even the Americans have been able to do.
So setting up factories in North Korea (where labour is cheaper than South) will mean ability to manufacture at lower cost. This would increase South Korea's global competitiveness. I do not foresee any economic problems in South Korea due to this as it survives on exports.
There may be some social problems which am unable to say much about as I do not know about the cultural differences. But perhaps the two countries were one till about 50 years back. That will smoothen the road.
The two nations can start with free trade & open borders, unification will follow.
Certainly even the Germans who had much less division between the two are still having social and economic issues between the two Germanies some thirty years after German Unification. Both Koreas will have cultural differences too. One way to resolve this issue seems to provide new government incentives to Southern ex-factory workers to move up north and get a job and house there. Certainly their new pay-check may be lighter than they used to be, but so will their cost of living in ex-North Korea will be. These human interactions could smoothen the division between the two Koreas.