Solved, I had to modify the DeleteMany method implementation to receive a FilterDefinition<TDocument> instead of an Expression<Func<TDocument, bool>>, so I could formulate and pass the following filter:
var practicesToDelete = request.Questions.Select(x => x.Practices).Distinct();
var filter = Builders<Question>.Filter.In(x => x.Practice, practicesToDelete);
var practicesToDelete = request.Questions.Select(x => x.Practices).Distinct();
var filter = Builders<Question>.Filter.In(x => x.Practice, practicesToDelete);