Well if I am looking for records for less than 1 percent of the population
You don't make much sense, Mark. Do you have an idea how many people there are worldwide who are descendants of protestant Germans, Dutch, French or Scots who lived in the area which is now Poland? The chance that the majority of protestant church books remained in Poland is quite low actually, given the fact that almost 400000 of them ended up in Moscow and are now scanned by the LDS, that loads of them were destroyed during the war and by the Poles immediately after the war, and that many more are kept in Berlin.
As far as the Catholic records all records can be found in Polish archives unless they were destroyed during the war or in the Polish uprising
A lot of old catholic church books were given back to Poland by Germany as late as 2001, and AFAIK there are still plenty left in the archives in Regensburg (I heard it's closed now) and Nuremberg, respectively.