Hey, I know this is a SPARQL question not specific to Jena, but I couldn't get an answer on public-sparql-dev, so I'll try my luck here: https://lists.w3.org/Archives/Public/public-sparql-dev/2016AprJun/0010.html
This is a real problem we have, triples end up in wrong graphs when we split one large graph into multiple per-resource named graphs. Martynas