Data Source used by script is not registered with server... Except that it is registered.

[jslinksy]

I have a python service that accesses an enterprise geodatabase via an SDE connection file. I can successfully run this script, however, when I analyze it in ArcPro before publishing it to the server I get "24032 Data source used by script <tool> is not registered to the server and will be copied to the server: <path_to_sde_file>". I am confused as to why I am getting this message because I have already taken the exact .sde file that the script references and registered it as a data store with the server. I can view the data store and validate it in the server manager. I don't want the data to be copied to the server, I want the service to reference the enterprise geodatabase. How can I get ArcPro to recognize that this .sde file in the script is registered as a data store for this service? 

EDIT: 
I believe that ArcPro thinks that this path in my python script is a folder, NOT an .sde file. When I click the "Register Data Source With Server" after analyzing the script, it pulls up the form to register a folder (screenshot below), which looks different than the form to register a database. I don't know why this would be happening as the path in my script is clearly an absolute path to the .sde file. The path in my script is below. The path does not include the <> characters, I have obfuscated some of the values.

connection_file = r'C:\Users\<user>\Documents\ArcGIS\Projects\<project>\<connection_name>.sde'

Register folder menu (This is what pops up when fixing via the 'analyze' results):

Vs Register Database menu:

[ODWC_GIS]

A shot in the dark: are you currently signed-in to ArcGIS Pro using your Portal Admin credentials, or your ArcGIS Online credentials?

I know it's weird that my agency flips between the two for different actions, but it's the first thing I check when the Publishing to the Server Interface shows me unexpected options.

[jslinksy]

Hi @ODWC_GIS,

Thanks for the reply. I am signed in to ArcGIS Pro with my ArcGIS Enterprise login (which has admin privileges). We are running ArcGIS Enterprise 10.9.1. 

[TimothyMichalowskigeosyntec]

We have Enterprise 10.9.1 same and same issue started with me last Friday.  Suddenly one of our ArcGIS Servers 10.9.1 is having data registration / data store issues. A SQL SDE DB file is registered with the ArcGIS Server data store with a sde connection file, but then ArcGIS Pro notes that the layers are not registered using the same connection file.  Then when trying to register anew then the same message as you noted states that the registration to this SQL SDE DB already exists = Circular contradictory messages without resolution.  First message says layers in SQL SDE DB aren't registered, then attempting to register says the SQL SDE DB is already registered.  No resolution.

[JenniferLana1]

did you get any resolution to this issue?  We are starting to have the same issues, last week.   

[jslinksy]

No resolution yet.