Hey @jokk33, as @Anurag said --store-xids and --xidmap are two different flags. --store-xids creates edge xid(name of edge) from from newly inserted node to blank id passed in RDF. It doesn’t check if any node with same blank already exist.
You are correct --xidmap is the correct way to handle it and it has recently been added by @Anurag in bulkloader as well.
Were you running bulk loader with all files? It thats the case, it should have assign same uid to same blank node id. If not, please try running bulkloader passing all the files to it. I should work as expected.