I had a bad experience of merge. The result was that if I navigated to the person from one direction I got complete parentage, but not if I navigated to that person from another. Now I always say No to the question, even if the two names represent the same person. Instead I find using Fix Relationship Mistakes from the People menu much cleaner.

Copy over the information from where the individual appears as a child, say, to where s/he appears as a spouse (you can cut and paste notes, for instance), then delete the child. Staying with the deleted child's parents, click on People, then Fix Relationship Mistakes, then Attach Child. You get your index of names, from which you select the name of the spouse onto whom you have just loaded all the information. Click on it, they say Yes to attach.

Similarly, where you have made a mistaken merge, detach the name as a spouse or a child, fill the gap you have just created with the name, which will as yet have no information to go with it, transfer the relevant information across and attach and detach relatives as necessary using Fix Relationship Mistakes.