MongoDB does not get updated - mongodb

Question

I use Doctrine 2 ODM\MongoDB (this and dependencies all latest from GIT) + PHP Mongo extension (v1.1.4) + Mongo (v1.8.3 x64 latest)
In several cases it happens that when I change an entity, it does not get updated
In an embedded entity I have a back reference to it's parent, to solve http://groups.google.com/group/doctrine-dev/browse_thread/thread/016422b2cc9dcec9?pli=1 (How to get parent document inside embedded document?) without using internal functionalities like UnitOfWork - this MAY or MAY NOT be relevant, I do not know... I would hope that not (my question whether it could went unanswered on the IRC so far)
However a single change in one of Character's embedded documents triggers these queries (should really be relevant only to it, there's been flush before it and a condition inside the logger on the flag that was set again right before the change)
Logger dump:
array(6) {
"update" => TRUE
"query" => array(1) {
"_id" => MongoId(1) {
"$id" => "4e3143be662c32400d000006" (24)
}
}
"newObj" => array(1) {
"$set" => array(2) {
"components.destructible.hp" => 99.28706276
"options.character" => array(3) {
"$ref" => "characters" (10)
"$id" => MongoId(1) { ... }
"$db" => "nuclearRain" (11)
}
}
}
"options" => array(0)
"db" => "someDB" (11)
"collection" => "characters" (10)
}
array(6) {
"update" => TRUE
"query" => array(1) {
"_id" => MongoId(1) {
"$id" => "4e553306662c32680800054b" (24)
}
}
"newObj" => array(1) {
"$set" => array(1) {
"createdBy" => array(3) {
"$ref" => "characters" (10)
"$id" => MongoId(1) { ... }
"$db" => "nuclearRain" (11)
}
}
}
"options" => array(0)
"db" => "someDB" (11)
"collection" => "worlds" (6)
}
array(6) {
"update" => TRUE
"query" => array(1) {
"_id" => MongoId(1) {
"$id" => "4e553306662c32680800054c" (24)
}
}
"newObj" => array(1) {
"$set" => array(1) {
"world" => array(3) {
"$ref" => "worlds" (6)
"$id" => MongoId(1) { ... }
"$db" => "nuclearRain" (11)
}
}
}
"options" => array(0)
"db" => "someDB" (11)
"collection" => "games" (5)
}
Initialization code: http://pastebin.com/1dKagqry
"components.destructible.hp" => 99.28706276 is the core part -> yet this change is never reflected in the DB
there is no php error/exception triggered
mongo's log shows no errors
generally the Mongo and Doctrine\ODM\Mongo runs fine, entities get persisted, updated, deleted...
Where can I search further or what can I do to solve this issue
Thank you

Answer 1

It is awkward, but the issue is that I wanted the EmbeddedDocuments indexed (like associative array)... this was however done on an actual Doctrine-maintained property, so it triggered re-pushing the EmbeddedDocument, discarding the changes

Answer 2

$friend = Zend_Registry::get('doctrine')->getDocumentManager()->createQueryBuilder('App\document\Message')->update()->field('unread')->set(TRUE)->field('viewer_id')->equals(10001)-> getQuery(array('multiple' => true))->execute();