The recent correction #1003 to the existing Calistoga boundary appears to be for the boundary that was updated when Crystal Springs of Napa Valley was established.
https://www.ecfr.gov/compare/current/to/2024-01-01/title-27/chapter-I/subchapter-A/part-9/subpart-C/section-9.209
It's not uncommon for adjacent boundaries to change when a new AVA is established. It's better to have one person work on something like this rather than two people nearly nine months apart.
- One Federal Register document
- One GitHub issue (Add Crystal Springs of Napa Valley, Update Calistoga)
- One person working on one QGIS project
- One person submitting one PR
Then both intrinsically related changes get merged into the dataset at the same time, as they should.