When a feature service contains features with empty geometry, upon exporting the feature service to a file geodatabase, the features with the empty geometry are assigned the coordinates of the previous objectID.
Workaround 1: Export the data to a shapefile, then convert the data to a file geodatabase. This does not work if the service contains attachments or related tables.
Workaround 2: Make the service editable and update the features through REST to give valid geometry to the features (http://resources.arcgis.com/en/help/arcgis-rest-api/index.html#/Update_Features/02r3000000zt000000/). This requires knowing the object ID(s) of the feature(s) with empty geometry, and either knowing the X and Y coordinates of where the feature is located or assigning a dummy value.
1. Through REST, go to the Update Features operation (example: http://sampleserver3.arcgisonline.com/ArcGIS/rest/services/SanFrancisco/311Incidents/FeatureServer/0/updateFeatures)
2. In the text box, use the following syntax:
[
{
"attributes" : {
"objectid": 1
},
"geometry" : {
"x" : -100.5,
"y" : 40.5
}
}
]
3. Repeat for all of the affected records.