(I hope this is the right place to ask this question).
Looking at https://github.com/jsonld-java/jsonld-java/blob/master/integration/jena/src/main/java/com/github/jsonldjava/jena/JsonLDReader.javait seems that the current JSON-LD reader does not copy the prefix definitions into the target Jena model, even though the writer is correctly creating them.
Thanks Holger
