Hi @GGThornhill
Is it possible that your control points have the same names in both components (and they are not the same points)?
If so, try to rename the names.
Also, it depends what kind of artefact are you scanning… If it is too narrow, there could be some issues to merge such components. Sometimes, you will need to do it in some 3rd party application, as if there is a weak overlap, then it won’t be possible to merge such parts. Or, you can use more shared control points to merge them together.