json-schema-to-openapi-schema | little NodeJS package to convert JSON Schema | REST library

The problem you have is that you are applying inference tooling over a multi-step conversion. As you have found, inference tooling is inherently fussy and will not work in all situations. It's kind of like playing Chinese whispers - every step of the chain is potentially lossy, so what you get out the other end may be garbled.

Based on the alternative approach you suggest, I would suggest a similar solution:

OpenAPI is, rather obviously, an API definition standard. It should be possible for you to take a code first approach, composing your API operations in code and exposing the types generated from XJB. Then you can use Apiee and its annotations to generate the OpenAPI definition. This assumes you are using JAX-RS for your API.

This is still a two-step process, but one with a higher chance of success. The benefit here is that your first step, inferring your XSD types into java types, will hopefully have very little (if any) impact on the code which defines your API operations. Although there will still be a manual step (updating the models) the OpenAPI definition will update automatically once the code has been rebuilt.