There are a couple ways to fix this, this is just one, with testing cheats enabled.
I am assuming in kingdom mode (not in a quest) that you see the merchant house is unoccupied, if so then create a new merchant (create a sim).
Start a quest with the new merchant. While playing as new merchant find your old merchant on screen, shift key+left mouse click on your old merchant and then select 'add to active family' (as this is your main objective).
Then find and do the same with the wife. Save your game as a new file.
Now, either keep the new merchant as a live-in family member or kill off the new merchant (send them to the pit),
or even move him to the village as a local trader; you can do this by selecting a villager npc (shift+right click as this will make them the active sim), and then use the villager to 'add to active family' (thus removing the new merchant from merchant house to live as a playable villager).
Save your game as a new file.
Hope this helps. If this doesn't work for you then describe where this advice fails, at the problematic step.