MongoDB document found on replica set but not in mongos

I have a sharded cluster: two shards – each a replica set with 3 nodes, and a config replica set (with 3 nodes).

I sharded my cluster by two collections in the same database:
– players.user_id – it's a hashed shard key
– users._id – an unhashed shard key

I wanted to shard users._id with a hashed key. So I followed these steps https://docs.mongodb.org/manual/faq/sharding/#can-i-change-the-shard-key-after-sharding-a-collection.

Notes:
1. Since the users collection was already sharded, each backup and restore was done on the same replica set; the backup & restore was done with data dumps.
2. After I dropped my users collection I created the collection and added the _id: hashed index on it and then configured the sharding with _id: hashed.
3. After the sharding I restored the data and ran my application, which created other indexes, a _id: 1 index and other indexes – some of them being sparse.

After this I have a lot of users (like half of them) which I can find querying the mongod on any of my replica set nodes (from where I backed them up and restored), but not querying the mongos.

Also, my counts are wrong:

mongos> db.users.find({}).length()
355
mongos> db.users.find({}).count()
664

repl-set-1:SECONDARY> db.users.find({}).length()
36
repl-set-2:SECONDARY> db.users.find({}).length()
628

I have balacing enabled, all of my replica sets nodes are in sync within their replica sets, each server can reach the others, I don't have timeouts or other visible configuration problems.

mongos> sh.status()
--- Sharding Status ---
  sharding version: {
    "_id" : 1,
    "minCompatibleVersion" : 5,
    "currentVersion" : 6,
    "clusterId" : ObjectId("...")
}
  shards:
    {  "_id" : "repl-set-1",  "host" : "repl-set-1/repl-set-1-1:27017,repl-set-1-2:27017,repl-set-1-3:27017" }
    {  "_id" : "repl-set-2",  "host" : "repl-set-2/repl-set-2-1:27017,repl-set-2-2:27017,repl-set-2-3:27017" }
  active mongoses:
    "3.2.1" : 3
  balancer:
    Currently enabled:  yes
    Currently running:  no
    Failed balancer rounds in last 5 attempts:  0
    Migration Results for the last 24 hours:
        No recent migrations
  databases:
    {  "_id" : "mydb",  "primary" : "repl-set-2",  "partitioned" : true }
        mydb.players
            shard key: { "user" : "hashed" }
            unique: false
            balancing: true
            chunks:
                repl-set-1  2
                repl-set-2  2
            { "user" : { "$minKey" : 1 } } -->> { "user" : NumberLong("-4611686018427387902") } on : repl-set-1 Timestamp(2, 2)
            { "user" : NumberLong("-4611686018427387902") } -->> { "user" : NumberLong(0) } on : repl-set-1 Timestamp(2, 3)
            { "user" : NumberLong(0) } -->> { "user" : NumberLong("4611686018427387902") } on : repl-set-2 Timestamp(2, 4)
            { "user" : NumberLong("4611686018427387902") } -->> { "user" : { "$maxKey" : 1 } } on : repl-set-2 Timestamp(2, 5)
        mydb.users
            shard key: { "_id" : "hashed" }
            unique: false
            balancing: true
            chunks:
      repl-set-1    2
      repl-set-2    2
            { "_id" : { "$minKey" : 1 } } -->> { "_id" : NumberLong("-4611686018427387902") } on : repl-set-1 Timestamp(2, 2)
            { "_id" : NumberLong("-4611686018427387902") } -->> { "_id" : NumberLong(0) } on : repl-set-1 Timestamp(2, 3)
            { "_id" : NumberLong(0) } -->> { "_id" : NumberLong("4611686018427387902") } on : repl-set-2 Timestamp(2, 4)
            { "_id" : NumberLong("4611686018427387902") } -->> { "_id" : { "$maxKey" : 1 } } on : repl-set-2 Timestamp(2, 5)

My questions are:
1. How can I debug this? I tried a lot of things…
2. What may cause this? The way that I backed up and restored data, the presence of sparse indexes?
3. How can I fix this, if I can?