The new secondary index API does not notify indexes of single-row or slice deletions unless specific columns are deleted. I believe the problem is that in SecondaryIndexManager.newUpdateTransaction(), we skip indexes unless index.indexes(update.columns()). When no columns are specified in the the deletion, update.columns() is empty, which causes all indexes to be skipped.
I think the correct fix is to do something like this in the ModificationStatement constructor:
However, I'm not sure if that may have unintended side-effects. What do you think, slebresne?