A FAT filesystem won't help the wear - if anything it will make it worse since the diectory and FAT structures need updating as well as the data.
I'm not 100% sure of the EPCS64 chips, some flash chips have a sector erase (to all 1's) and allow writes to individual words to clear bits. There is no requirement to do all the writes at once.
So you can write the 'new' data further down the 64k sector (into an area that is still 0xff), then clear some bits of the header of the old data to mark it invalid. The erase then only need be done when you are getting near the end of the flash sector.
I've that technique for 'environment' data - a 32 bit word held 3 bytes tag + 1 byte length (in words). Write sequence was: 0xffffff | length, data, tag | length, 0 | old_length (over old tag).