Auto-Number not available as external ID in Data Loader

While it is possible to use an auto-number field as an external ID field, Data Loader does not support its use for the Upsert functionality.

The Upsert command performs an "insert or update" function, depending on whether or not Data Loader finds an existing record in the system. Since auto-number fields cannot be inserted or created, Data Loader does not allow you to match by this field due to the possibility that the upsert will need to insert new data.

In addition, Data Loader only displays fields that are either create-able or update-able. Since autonumber fields are not create-able or update-able, they do not show in the options available in Data Loader. This is intentional behavior to avoid errors that would result from Data Loader attempting to create or update this field. 

As a work around, consider changing the field type can be switched to Text for the time of the update and then back to Auto number again. It is strongly recommended that you backup the data prior to each field type change in case unexpected results occur during the change.