Create a conditional TTL in mongo

I would just add another field. It's not that much data:

{
'_id' : 123456789,
'createdDate' '<date when mail was sent or the request was created>',
'scheduledDate' : '<time for which mail is scheduled>'
'expires': '<Date or NULL>'
}

Add a TTL index of 0 seconds to the expires field. Don't add a TTL to the other dates.

The following examples are in Mongoose (an ORM for Node) but the ideas should carry over to whatever framework you're using:

A default value

You could add a default value to the expires field with the value of 'created date + 2 days'.

{
  type: Date,
  default: function() { 
    return new Date(Date.now() + 1000*60*60*24*2);
  }
}

A different expire date for your scheduled tasks

Just set the date explicitly:

myNewDocument.expires = new Date( scheduled + ... );

Or change the function that sets the default value:

function() {
    if(this.get("type") === 2) {
      return scheduled_date_plus_2_days;
    } else {
      return created_date_plus_2_days;
    }
}

No expiry at all

Set the field to NULL:

myNewDocument.expires = null;

---

This way, you have the ability to choose a different expiry for normal emails, important emails, scheduled ones, etc. If you're on time, you can even set the expires field to NULL to cancel the automatic deletion.
The only caveat is that if you change the scheduled time, you'll need to update the expires field.

You can just create a TTL index on scheduledDate, if the value is zero it will not be deleted. According to the documentation, if the indexed field in a document is not a date or an array that holds a date value(s), the document will not expire.

Using Mongo 3.2 I have verified this is indeed the case using this test collection:

db.data.drop()
db.data.save({scheduledDate: 0})
db.data.save({scheduledDate: new Date()})
db.data.save({scheduledDate: new Date()})
db.data.createIndex( { "scheduledDate": 1 }, { expireAfterSeconds:1} )

When using this collection all new Date() entries get removed , whereas the first record with the zero value remains

As of MongoDB 3.2, it is also possible to add a partial TTL index using a specified filter expression. In case if you need to remove only normal not scheduled emails, you could use the following:

db.email.createIndex( {createdDate: 1}, {
    expireAfterSeconds: 172800, // 2 days
    partialFilterExpression: {
        scheduledDate: 0
    }
});

Note that partialFilterExpression has restrictions on possible filter conditions: https://docs.mongodb.com/manual/core/index-partial/