Setting user-observer pairing via upload or API with an active SIS integration

[apixtech]

Prior to our sync to Aspire (Utah's SIS system) I was able to upload a file via SIS uploads or use the API to pair success coaches with their students as observers. 
However, since the integration when I run it in test it generates duplicate users in a observer/user paring instead of paring existing users. 
I've checked the documentation and tried the git hub solutions, I'm using a downloaded file to ensure the ID's are exactly correct, and the formatting doesn't give me any errors. The API executes successfully without errors. I am able to perform other operations on existing users, like password resets, without issue. 
No matter what I try, I can't get it to pair the existing users instead of generating new ones. 
I do have my old documentation in a SOP, so I'm nearly positive I"m doing the exact same thing I did pre sync, but I can't be 100% sure as this is really a once a year thing. 
Generating code via the API works great, and we use this for parents but it would be overwhelming to pair the coaches with students 1 by 1. 
Suggestions? Even ideas about what to add to logging to troubleshoot would be helpful. 

[Code-with-Ski]

@apixtech 

For some clarification, is the download file you are using an SIS export of users?  Also, are the other operations (like password resets) that are successful, things you are doing with an SIS users import?

In addition, since you are having issues on "test", have you tried using the "beta" server to see if you experience the same issue? It may be good to report the error to Canvas Support too as that does seem like unexpected behavior.  I would expect it to give an error of a user not being found rather than creating new users.

As for the API approach, what are you using to make the API call?  If it is already a script, and you have it working for one, you should be able to make a script to read a file with the IDs to use for pairing and a loop to make the API call for each pair of user IDs.  Even though this would technically still make the API calls 1 by 1, the script handles this repetitive process, and you would just need to provide a properly formatted file with the IDs for pairing.