ve.dm.MWReferenceNode contains a comparison of element linear data done using a simple object reference equality check (===). In debug mode where objects are frozen with ve.deepFreeze - this check always returns false and breaks toDomElements.

The first attempt to fix this resulted in T296044.

Testing

1. Open VE in debug mode (?veaction=edit&debug=true)
2. Create a basic reference with content (e.g. <ref>Foo</ref>)
3. Inspect the wikitext produced (either by: switch to source mode, showing wikitext changes, or saving)
4. Observed: The reference is now empty: <ref />
5. Expected: The reference contents is preserved