I have used ORDO for over 10 years.
In the last release it looks like many intermediate nodes are suddenly children nodes of "Disease" only:
https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_377788&lang=en&viewMode=All&siblings=false
For example: Genetic non-syndrome obesity:
https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_98267
Which is now a child only of "disease" and has no child terms of its own.
Here's another example: Autosomal dominant secondary polycythemia
https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_247511
Which is also now a child only of "disease" and has no child terms of its own.