The patch3ps3.cpk is update CPK that was available digitally for Persona 5 a few days following launch. It contained two BF files that had been altered in some way.
Modding
For the Japanese version, patch3ps3.cpk is the optimal CPK to use as a replacement, seeing as it overrides all other CPK files, thus covering the whole filesystem of P5. It's also the smallest CPK, less than 1 MB in size and completely inessential to running the game or using DLC.