Especificando a posição real do documento incorporado como este:
// update _id field of first author
collection.update({'_id': "4f44af6a024342300e000001"},
{$set: { 'authors.0._id': "1" }} )
Ou via operador posicional :
// update _id field of first matched by _id author
collection.update({'_id': "4f44af6a024342300e000001",
//you should specify query for embedded document
'authors._id' : "4f44af6a024342300e000002" },
// you can update only one nested document matched by query
{$set: { 'authors.$._id': "1" }} )
