When they first put the limit on the zones a while back, I had files that had more than the limit that were automatically imported into the new PPS, that would still work. I made the mistake of deleting some of the zones, to where I had fewer than the limit. Then I couldn't add them anymore.
I recommend you backup your files, try the PPS, and see if you're still able to work with it. If you want to send me a copy of them, I could try it with the latest version of PPS and firmware that I've been using.