I'd suggest using Select by Location, using the layer with fewer points to select the layer with more points.
https://pro.arcgis.com/en/pro-app/3.1/help/mapping/navigation/select-features-by-location.htm
This should give you the points in the more points layer that overlap the fewer points layer.
Then, in the more points layer, open the attribute table and click the button to switch the selection.
This gives you the features in the more points layer that are not in the fewer points layer.
You can export this to its own new feature class, and then append that feature class to the fewer points layer.