Github user stain commented on the issue:

    https://github.com/apache/commons-rdf/pull/30
  
    Thanks @afs , that makes sense, `JenaGraphImpl` was indeed using 
`graph.delete()`. 
    
    I have fixed in both `JenaGraphImpl` and `JenaDatasetImpl`.  See comment - 
do you think there is much performance gain from not splitting into pattern but 
passing the original Jena Triple (safe only when there's no Literal object with 
langtag) - or shall we always use the pattern?
    
    (e.g. would Jena TDB do things like get an internal Triple row ID out of 
the jena `Triple` for faster delete?)
    
    I added tests for Dataset that reveals that statements in default graph 
come back from Jena in the named graph `<urn:x-arq:DefaultGraph>` - that's a 
separate bug in `JenaDatasetImpl` and the converters - we should represent that 
always as `Optional.empty()` in Commons RDF land.



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