Usually the points get credited at the same time if both flights are on the same ticket and transiting.

I would suggest the same, removing your frequent flyer number from the booking altogether first. If your flying PEY/Econ, then manually show your membership card at check-in, lounge, boarding gate so you can still enjoy the ground privileges.

After you've flown on the flights, submit the claim for your first flight and wait for that to clear. Once the points are credited and your tier upgraded, do the same for the 2nd flight so it can be earned under your new tier.