MongoDB stage LIMIT_SKIP

Question

I migrated from MongoDB to AWS DocumentDB and I'm having some issues with query performance. Running a profile I found several queries taking a laaaarge amount of time, far beyond a couple of seconds. I tried to understand with the doc what some of those stages mean like LIMIT_SKIP and understand why they're taking so long. Specially those that are updates against _id.

As context I'm using Mongoid 6.4.4 with AWS Document DB.

Here are the profile I get and below the models stats:

    {
    "op": "update",
    "ts": 1592322527421,
    "ns": "mytable.paths",
    "command": {
        "q": {
            "_id": "5ee8e93217f3830001cf9765"
        },
        "u": {
            "$set": {
                "last_active_at": "2020-06-16T15:48:19.774Z",
                "updated_at": "2020-06-16T15:48:19.774Z"
            }
        }
    },
    "nMatched": 1,
    "nModified": 1,
    "protocol": "op_query",
    "millis": 27643,
    "planSummary": "IXSCAN",
    "execStats": {
        "stage": "UPDATE",
        "nReturned": "0",
        "executionTimeMillisEstimate": "27638.070",
        "inputStages": [
            {
                "stage": "LIMIT_SKIP",
                "nReturned": "1",
                "executionTimeMillisEstimate": "27637.167",
                "inputStage": {
                    "stage": "IXSCAN",
                    "nReturned": "1",
                    "executionTimeMillisEstimate": "0.046",
                    "indexName": "_id_",
                    "direction": "forward"
                }
            },
            {
                "stage": "IXSCAN",
                "nReturned": "1",
                "executionTimeMillisEstimate": "27637.510",
                "indexName": "_id_",
                "direction": "forward"
            }
        ]
    },
    "client": "10.70.11.85:53788",
    "user": "avion_admin"
}

Another very similar:

    "op": "update",
    "ts": 1592336823405,
    "ns": "mytable.groups",
    "command": {
        "q": {
            "_id": "5cf599047ce44a2eb43f8bb9"
        },
        "u": {
            "$set": {
                "empty": false
            }
        }
    },
    "nMatched": 1,
    "nModified": 0,
    "protocol": "op_query",
    "millis": 158338,
    "planSummary": "IXSCAN",
    "execStats": {
        "stage": "UPDATE",
        "nReturned": "0",
        "executionTimeMillisEstimate": "158329.635",
        "inputStages": [
            {
                "stage": "LIMIT_SKIP",
                "nReturned": "1",
                "executionTimeMillisEstimate": "2.686",
                "inputStage": {
                    "stage": "IXSCAN",
                    "nReturned": "1",
                    "executionTimeMillisEstimate": "2.672",
                    "indexName": "_id_",
                    "direction": "forward"
                }
            },
            {
                "stage": "IXSCAN",
                "nReturned": "1",
                "executionTimeMillisEstimate": "6.390",
                "indexName": "_id_",
                "direction": "forward"
            }
        ]
    },
    "client": "10.70.13.122:44162",
    "user": "avion_admin"
}

And this one I can't even get where is being done:

{"op":"query","ts":1592372335740,"ns":"mytable.devices","command":{"$truncated":"{\"find\":\"devices\",\"find\":\"devices\",\"filter\":{\"$and\":[{\"_id\":{\"$in\":[ObjectId('5c35814ce5e09d5b6e5ca432')...},"cursorExhausted":true,"nreturned":1,"responseLength":25,"protocol":"op_query","millis":97669,"planSummary":"IXSCAN","execStats":{"stage":"SUBSCAN","nReturned":"1","executionTimeMillisEstimate":"24956.315","inputStage":{"stage":"LIMIT_SKIP","nReturned":"1","executionTimeMillisEstimate":"24956.247","inputStage":{"stage":"IXSCAN","nReturned":"1","executionTimeMillisEstimate":"24956.246","indexName":"status_1","direction":"forward"}}},"client":"10.70.11.237:45532","user":"avion_admin"}

Models:

{
    "ns" : "mytable.paths",
    "count" : 60192,
    "size" : 16974144.0,
    "avgObjSize" : 282.5631,
    "storageSize" : 45039616.0,
    "capped" : false,
    "nindexes" : 4,
    "totalIndexSize" : 68542464.0,
    "indexSizes" : {
        "_id_" : 17072128.0,
        "device_id_1" : 15196160.0,
        "location_id_1" : 18317312.0,
        "registration_id_1" : 17956864.0
    },
    "ok" : 1
}

{
    "ns" : "mytabke.devices",
    "count" : 78450,
    "size" : 57739200.0,
    "avgObjSize" : 736.49595,
    "storageSize" : 217628672.0,
    "capped" : false,
    "nindexes" : 9,
    "totalIndexSize" : 1194442752.0,
    "indexSizes" : {
        "_id_" : 30179328.0,
        "energy_changed_at_1_intervals_up_to_1" : 83402752.0,
        "group_ids_1" : 168148992.0,
        "location_id_1" : 21880832.0,
        "location_id_1_avid_1" : 51593216.0,
        "pinged_at_1_features_1" : 148955136.0,
        "status_1" : 163741696.0,
        "status_1_features_1_last_active_at_1_pinged_at_1" : 264159232.0,
        "status_1_last_active_at_1_since_active_at_1" : 262381568.0
    },
    "ok" : 1
}

{
    "ns" : "concourse.groups",
    "count" : 11198,
    "size" : 6456828.0,
    "avgObjSize" : 576.605465261654,
    "storageSize" : 38461440.0,
    "capped" : false,
    "nindexes" : 5,
    "totalIndexSize" : 810500096.0,
    "indexSizes" : {
        "_id_" : 1794048.0,
        "device_ids_1" : 785743872.0,
        "dim_1_mixed_1" : 15261696.0,
        "location_id_1" : 3129344.0,
        "location_id_1_avid_1" : 4571136.0
    },
    "ok" : 1
}