Figured it out.
- Open Health
- Select Browse
- In search box enter the state where the vaccine record comes from. I'm in California so I start to type 'cali' and a record for the state health dept. shows up.
- Select that entry, then click on more time on details, then delete source and data button.
- Then re-snapshot the QR code you .gov record sent you. i.e. https://myvaccinerecord.cdph.ca.gov/
- It should add in fine, without the duplicate message and create the entry in wallet.
Good luck, and Apple you should really fix this. Got a new phone and it didn't transfer over my vaccine record to wallet, even though the entry was in my health app (although hidden in a weird place). Also the state COVID vaccine doesn't show up under my immunizations, so took me a while to figure out where it was saved. Overall, great feature, love the vaccine card on my phone, but this was a bit of work.