In doctrine/data-fixtures, when a collection is "purged", it is totally dropped and indexes are recreated.

https://github.com/doctrine/data-fixtures/blob/f65b353922b7ac48f360428e19b22fcce5aba134/src/Purger/MongoDBPurger.php#L47 

Solution 1:

• Call SchemaManager::createCollection() before 
  ensureIndexes(), and probably also createSearchIndexes()
• This will create new encryption keys

Solution 2:

• Remove all data using deleteMany([])
• May be slower