You mentioned that the letter you received was a"letter with a reference number and the missing document required". The FAQs page, number 1 is very clear:
"The new measures apply to you if, by August 1, 2013, you received one of the following documents from the Ministère:
an acknowledgement confirming that your file has been opened and the fees received;
an acknowledgement as well as a letter asking you to provide missing documents or conforming documents in order to process your application."
evidently, your situation is the second one, so new rules will apply to you.
In my opinion, since they mentioned in their website that some verifications will need to be done before your file can be processed, it is possible that they have just looked at the completeness of your file at this point, and has not yet started processing. If they had already started processing or reviewing, chances are, they would be asking for the documents using the "Intention to Refus" letter, as quoted:
"You received a letter entitled “Intention de refus” (intent to refuse the application), informing you that you must submit other documents or information that will allow us to continue to review your file;"
That is not the letter you have received so more than likely, processing has not yet started on your case as this is the letter given if documents are missing during their review of your application. Question no. 3 just talks about the application of the 20,000 cap not being applicable to applications submitted before Aug.1. It seems to be separate from the issue of which set of rules will be applicable to you.
