We have a run at rate coming up soon with an important visit. we are a 4th tier supplier and we have changed our process in relation to our ppap submission (this was due to our supplier --3rd tier) should we protect them somehow or just explain the situation and hope for the best? please reply soon!

I would suggest that you prepare all the documentation to match your current process, this is checked at the run@rate.

Send a copy to your customer with a warrant which shows change of process.
You should have done this anyway!

Even if you do not get approval from the customer in time the documentation will show you have sent it.

Tell your customer that you are sending this up to date PPAP.

Good luck!