[Bug] Partial parsing drops versioned model node after schema.yml change (v2 ‘not found’)

### Is this a new bug in dbt-core?

- [x] I believe this is a new bug in dbt-core
- [x] I have searched the existing issues, and I could not find an existing issue for this bug

### Current Behavior

In dbt Cloud, with partial parsing enabled, editing a schema.yml file for a versioned model causes dbt’s internal dependency graph (manifest) to lose the node for version 2 of that model.

Models involved (simplified):

```
8. Re-run with --no-partial-parse and confirm it succeeds again on the same code and checksum.

### Which database adapter are you using with dbt?

snowflake

### Additional Context

This looks closely related to dbt-core#11869 and internal TRIAGE-963 / INC-3298 (partial parsing + versioned models + schema.yml changes leading to “node not in the graph” errors), but:

- Model naming and versioning are correct here.
- v: 2 exists and compiles under full parse.
- The failure only appears after a partial parse where brightspace.yml is the only file detected as changed.