So, just so im clear, the "PB31IMG.zip" file unroots the phone. The "http://android.clients.google.com/pa...lease_sign.zip" file that gets renamed update.zip is the OTA update, and whether you do the update OTA, or through recovery its the same thing.
Once you are unrooted, updated, and rooted again, can you wipe those files from the SD card?