We have both indexes in YaCy, Lucene/Solr and kelondro. The kelondro index is used only when YaCy operates in p2p mode and it manages the fragments that are exchanged in the p2p transmissions. Think of it as a “dissolvable” index: when p2p transmissions are done, fragments of the index are taken out and transmitted to other peers.
A search in the p2p index is done on both, solr/lucene (locally) and kelondro (locally and remote). Searching the local kelondro index will access those parts that have been transmitted by other peers to your own peer.
So having two indexes (where one “dissolves” over time) ensures that you always own our own data (what you crawled, in the solr/lucene index) while having a distributed access to the p2p index (from what has been moved to your peer).