The PPAP Manual states we must keep a master part and label it accordingly. Currently we keep 6 pieces from the PPAP,and the next production run we keep 6 new ones from that order and throw the old six away. None of them are specified as master parts.
Are we in compliance?

There are 2 seperate issues as I see it.
PPAP master samples should be kept as examples of the parts submitted, the parts that you keep afterwards from production are to help you if you have a problem later with this specific production lot.
I would suggest that you keep more than the latest samples but at least a year or two backwards.
You must keep master samples seperately as a different subject

My two cents worth here is to say talk to your customer's supplier QA activity and ASK what they want SPECIFICALLY. I say this because I have seen different requirements from customers. In one case PPAP sample retention time and number was dictated by the size of the part (in that case it was hoods which were metal stamped). Doesn't hurt to check with your customer.