Just to give you guys some peace of mind, let's say your application was delivered to CIC on May 15th (as per the records of your courier company) and now you are waiting for AOR. The 4/6 rule then kicks in on June 1st (just an example only as the exact date is still unknown as of now) and later you receive the AOR on June 5th, the letter would say that we received your application on May 15th (and not June 5) cuz that's when CIC had officially received your application no matter when they opened it and they found out that it meets CIC's minimum basic requirement to consider your application for processing. Therefore, your application will be processed under 3/4 rule since it was complete and free from errors and was received by CIC at the time it was the 3/4 rule that was in force.
However, God forbid instead of getting AOR you receive your package back, on the grounds that it did not meet their minimum basic requirement, then for them it's as good as never received by them even though you have paid the fee in full. You will then be asked to resubmit the whole thing all over again with the correction. Now let's say the application was resubmitted after the required correction to the CIC on June 15th when 4/6 rule has already come into effect on June 1st (for example only) and at that point even if CIC finds all the documents in order, they will now see if the applicant has completed 1460 days (and not 1095 days) on the day he signed the new application since on June 15th the minimum residence requirement is 1460 days and not 1095 days anymore, therefore, the application will again be returned due to insufficient residence days. Hope this makes sense now.
Just to give you an example, a friend of mine sent his application to CIC last year with the old fee, while the application was in transit, CIC increased the processing fee, the day they received it the fee had already changed, they then returned the whole package back to him asking him to resubmit the application with the new increased fee.
Rest assured, if you guys receive your AOR (on your existing package that you have recently mailed) now or even after the rule changes to 4/6, your application will still be processed under the old 3/4 rule. The risk is only if your application is returned due to any error in your application or incomplete documentation.
Good Luck and just be positive that you don't get your application returned but receive your AOR instead even though it gets delayed