Rewrite all your UUIDs, that accidentially have been saved as BinData(3, "") as BinData(4, ""). But be careful! This script only takes one implementation of the three (Python, Java, C#) and treats all BinData(3, "") datasets like that. This can damage your data if you don't know what you're doing.

mongodb-replace-UUID-BinData3-by-BinData4

// Load this script: https://github.com/mongodb/mongo-csharp-driver/blob/master/uuidhelpers.js
// Start your mongo-shell with this script: mongo --shell uuidhelpers.js

// Find out what type of UUID it was. In my case it was PYUUID(). But it could (in your case) also be CSUUID() or JUUID().

db.tests.find(function() { return this.orderId.subtype() == 3 }).snapshot().forEach(function(elem) {
        db.tests.update(
            {
                _id: elem._id
            },
            {
                $set: {
                    orderId: UUID(elem.orderId.toPYUUID().substr(8,36).replace(/-/g,""))
                }
            }
        )
})