In working with HOT task #1357 I came across lots of buildings as points only.
I added polygons, some of which contained the previous added points.
JOSM gives a warning.
Here is a small residential area with the issue. https://www.openstreetmap.org/#map=19/6.15721/-10.22145
I assume this error is the one you referred to in your original posting. You either need to delete the nodes, or merge them into the outline.
Personally, I would try to retain the original node as a relevant features of the building, moving it if necessary. My preference, if that information is available, is to make it the main entrance of the building. I prefer that so that any reference to the node will still produce a reasonable result.