I think this is related to the problem I’m seeing in this post:
My case has the additional wrinkle that it’s ‘deleting’ markers that aren’t even on the part being scanned (so I don’t need it to do any marker removal magic anyway), but I’m also seeing that when it is removing those markers, its making holes in every scan, not just the ones affected by the markers. Effecgively its removing the markers from the finished mesh, not the source clouds.
So I wonder… if you’ve manually delete the scanned markers from the point clouds, leaving holes in the point cloud already, can you then go and edit the marker data associated with each scan, to delete the marker points, and then remesh? Without the marker data, I suspect it won’t think it has to make extra holes in things, and will just let the data from the other scan fill in the gap.