Dovresti usare $[] operatore posizionale multiplo, proverò a scrivere cosa dovresti usare per il codice che hai incollato:
var baseFilter = Builders<Project>.Filter.Eq("ProjectID": 1);
var update = Builders<Project>.Update.Set("ProjectTasks.$[i].Comments.$[j].CommentDescription", comment.CommentDescription);
var arrayFilters = new List<ArrayFilterDefinition>
{
/* change the type names here if they have different names, I just guessed */
new BsonDocumentArrayFilterDefinition<ProjectTask>(new BsonDocument("i.ProjectTaskID", projectTaskID)),
new BsonDocumentArrayFilterDefinition<Comment>(new BsonDocument("j.CommentId", commentID))
};
var updateOptions = new UpdateOptions { ArrayFilters = arrayFilters };
await Collection.UpdateOneAsync(baseFilter, update, updateOptions);