So if you manaully deleted the Indices from elstisearch, may i add that is probably not good idea, but if you have to do that then yes , the metadata would be in Monodb since you did not delete the indices from Grayloys web ui,
> use graylog;
switched to db graylog
> show collections
> db.index_sets.find().pretty();
That is for index failures not your index set.
Be warned the following command may or may not help, it might make things worse but I have had to use them before.
db.index_sets.drop()
OR
db.index_sets.drop( { writeConcern: <document> } )