Index nodes without assigned documents no longer disappear in my indices.
To recreate: create an index for a certain metadata type and set the metadata of a document to a previously unused value. After it was added to the index change the metadata value to another value (existing or not). The index node that was created before will remain in the tree without any assigned documents.
I’m running Mayan 4.6.3 but I think this started already earlier. A couple of releases back I reported a problem with disappearing index nodes that actually contain documents. I guess since the the implementation of this fix also the empty index nodes no longer disappear.