In MapInfo Pro:
Be aware of Spherical or Cartesian calculus (see "map options" dialog). Check if your tool calculates ObjectLen () or CartesianObjectLen() or SphericalObjectLen() and if it matches your map option calculus mode.
Some more info here:
If those overlapping features (points from the divided part) share the same location with features (points from the main layer) I will simply use the "Difference" from the Vector > Geoprocessing Tools > Difference.
This algorithm extracts features from the Input layer that fall
outside, or partially overlap, features in the Overlay layer. ...
I suppose that you have two layers with overlapping objects.
Processing → Extract by location.
Extract features from the main layer by comparing them with features from second layer. The predicate is disjoint.
After launch, you'll get the layer without points from the second layer.