When a feature class with overlapped points is published to ArcGIS Online, all the labels are shown when printing the map, even though the duplicate labels are removed from the Labeling Properties option in ArcGIS Pro.

Workaround

First workaround: Use a printing service from ArcGIS Enterprise 11.3 or below. Go to ArcGIS Online > Organization > Settings > Utility Services and replace the Esri default printing service.

Second workaround: create a new ID field and an Arcade expression for the labeling properties as shown below:

1) Add a new field in ArcGIS Pro (long type).

2) To assign values to this new field, please follow the steps below:

is equal to:

assign(!ID!)

Code Block:

labeled_group = {}

def assign(value):

global labeled_group

if value not in labeled_group:

labeled_group[value] = True

return 1

else:

return 0

3) From the labeling properties, for the Arcade expression, please add the following expression:

if ($feature.NewID == 1) {

   return $feature.ID;

} else {

   return "";

}

Please note in red that 'NewID' is the name that I assigned to my new field in step 1. Please update the name according to the name you assigned in this step. 

Please note in red that 'ID' is the name of the field that stores the values you want to label. Please update the name according to the name of your field. 

Attached is a set of two GIFs I made in order to demonstrate this workaround

Schritte zur Reproduzierung