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I just run nango migrate-to-zero-yaml, can I change the folder structure?

Yes, you can change the folder structure. You can move files, zod definitions, types, rename files, folders, etc. The results of the migration is just an example of how you can structure your project.

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I’m getting ZodXX is missing the following properties errors

If you are getting Zod errors, it’s most likely because you are using a different version of Zod than the one we use in our CLI. We currently require zod 4.0.5. If you have an overrides in your package.json or something that is changing the version of Zod, you will need to remove that. NB: nango compile will automatically update your dependencies to the version we use in our CLI.