This is all the DL legacy policy.
DL upgrades were in the form of paper certificates. You indicate you want to upgrade with the certificate and the class of service is changed and the certificate number was put in your reservation. When you arrive at the airport you surrender the certificate and the ticket is reissued.
Mileage upgrade works in similar fashion with the ticket either being reissued 72 hours prior to the flight or at the airport.
Both are/were intended to be customer-friendly policies. Once the certificate is redeemed and ticket is issued, the certificate can't be reused. Once the mileage upgrade is processed any changes would result in a fee or the use of a platinum waiver (Diamonds are now exempt from the mileage reissue fee)
Now that the upgrade certificates are electronic the former system isn't working so well. You might want to print out the electronic document to bring to the airport until all the ticket agents are harassed or threatened or forced to read all the company memos on how to handle the transaction.
The mileage upgrade process hasn't changed. Yeah I know it's archaic compared to how NW processed the same transactions. I am guessing in a couple pf months it will be streamlined. DL wants to win the JD Powers survey and this is definitely a major hiccup in achieving that.