Hey Kevin,
It looks like you can’t use auto-number fields as External ID’s for upserts: https://help.salesforce.com/articleView?id=000004514&language=en_US&type=1 and https://developer.salesforce.com/forums/?id=906F00000009CUSIA2.
Would you actually prefer to run an update? (Feels like upsert isn’t the right operation for an auto-number that’s generated in SF… what is the value you’re using in the cases that you want to insert new records?)
Taylor