Pull and addtoset at the same time with mongo

Starting in Mongo 4.4, the $function aggregation operator allows applying a custom javascript function to implement behaviour not supported by the MongoDB Query Language.

And coupled with improvements made to db.collection.update() in Mongo 4.2 that can accept an aggregation pipeline, allowing the update of a field based on its own value,

We can manipulate and update an array in ways the language doesn't easily permit:

// { "tags" : [ 1, 5, 8 ] }
db.collection.updateMany(
  { tags: 1 },
  [{ $set:
    { "tags":
      { $function: {
          body: function(tags) { tags.push(2); return tags.filter(x => x != 1); },
          args: ["$tags"],
          lang: "js"
      }}
    }
  }]
)
// { "tags" : [ 5, 8, 2 ] }

$function takes 3 parameters:

• body, which is the function to apply, whose parameter is the array to modify. The function here simply consists in pushing 2 to the array and filtering out 1.
• args, which contains the fields from the record that the body function takes as parameter. In our case, "$tag".
• lang, which is the language in which the body function is written. Only js is currently available.

If you're removing and adding at the same time, you may be modeling a 'map', instead of a 'set'. If so, an object may be less work than an array.

Instead of data as an array:

{ _id: 'myobjectwithdata',
  data: [{ id: 'data1', important: 'stuff'},
         { id: 'data2', important: 'more'}]
}

Use data as an object:

{ _id: 'myobjectwithdata',
  data: { data1: { important: 'stuff'},
          data2: { important: 'more'} }
}

The one-command update is then:

db.coll.update(
  'myobjectwithdata', 
  { $set: { 'data.data1': { important: 'treasure' } }
);

Hard brain working for this answer done here and here.

In case you need replace one value in an array to another check this answer:

Replace array value using arrayFilters

The error is pretty much what it means as you cannot act on two things of the same "path" in the same update operation. The two operators you are using do not process sequentially as you might think they do.

You can do this with as "sequential" as you can possibly get with the "bulk" operations API or other form of "bulk" update though. Within reason of course, and also in reverse:

var bulk = db.coll.initializeOrderedBulkOp();
bulk.find({ "tags": 1 }).updateOne({ "$addToSet": { "tags":  2 } });
bulk.find({ "tags": 1 }).updateOne({ "$pull": { "tags": 1 } });

bulk.execute();

Not a guarantee that nothing else will try to modify,but it is as close as you will currently get.

Also see the raw "update" command with multiple documents.