Did you figure it out and fix it yet? I'm not sure I'm following your problem exactly but it sounds like somewhere in your tree, you have a your 3rd great grandfather assigned as a child of the wrong parents. Is that the problem? Here's how to fix it:
1. First make a backup file in case something goes wrong. (Look at the menu bar across the top, under File, select Save a Backup Copy.)
2. In the Family View in your tree, select the Correct parents. Call these people Name 1 and Name2. Your 3rd great grandfather won't be shown as a child because that's what needs to be fixed.
3. Locate your 3rd great grandfather's name in the list on the right. Call him Name 3. Drag him (Name3) from the list on the right into the Children box under the correct parents (Name1 and Name2). You'll get a pop-up confirmation message saying "Add Name3 as a child of Name1 and Name2?" Select Add. Since he is already assigned to some other parents, you will get a pop up asking do you want to Duplicate or Move. Select Move. This will move him (AND EVERYONE BELOW HIM) to the correct family.
If you actually made TWO errors and assigned children to him that belong to someone else, just repeat the above for them.
Remember that Reunion comes with a Sample Family so you could PRACTICE this on the sample file first before you mess with your real family. (For example, move Caroline Bouvier Kennedy to be a child of her grandfather Joseph Patrick Kennedy.)
Bottom line, you can move people around wherever you want, you shouldn't have to re-enter any of your data.