How should schema markup be validated when the code passes a validator but search engines still ignore it?

Separate syntax validation from semantic validation.

First confirm the JSON-LD is valid and uses supported Schema.org types/properties. Then verify that the markup describes content visibly present on the page. Search engines may ignore technically valid markup that exaggerates, invents, or conflicts with the user-visible page.

Check entity identity carefully. Organization, LocalBusiness, Product, Article, Person, and other entities should use stable @id values where appropriate and connect through properties such as publisher, author, brand, mainEntity, about, isPartOf, and location. Do not create a new disconnected entity object on every page when the same real-world entity is being referenced.

Validate URLs, images, dates, prices, availability, addresses, and identifiers against the rendered page and canonical URL. For JavaScript-injected schema, confirm the rendered version is reliably available to bots and is not delayed behind interactions.

Then distinguish two goals:
1. Eligibility for a specific rich result, which requires Google's feature-specific documentation.
2. General machine-readable entity/context information, which can still be useful even without a visible rich result.

Use Search Console enhancement reports where applicable, but also crawl the site and inventory schema by template. Look for missing required fields, template drift, contradictory values, and duplicate entities.

A passing validator is the beginning of QA. The stronger standard is: accurate, visible, canonical, stable, connected, and appropriate to the page's actual purpose.