FFXIV_CHR00... folders -> your character config (in-game things). You can try to figure out which from the logs, but it's messy and not fun. But you can also totally copy files/back them up manually to sync your config as wanted.
FFXIV_CHARA_0X.dat -> your saved appearance. They are always in order. If you only saved a character appearance to slot 42, you'd have FFXIV_CHARA_42.dat.