I've gone through that and I only have one save folder here:
Library/Containers/com.mpdigital.pillarsofeternity/Data/Library/Application\ Support/Pillars\ of\ Eternity/Saved\ Games
Within that folder is:
410beccf-8906-4127-baef-7215f5891bbf autosave_0.savegame
410beccf-8906-4127-baef-7215f5891bbf autosave_1.savegame
410beccf-8906-4127-baef-7215f5891bbf autosave_2.savegame
410beccf-8906-4127-baef-7215f5891bbf quicksave.savegame
410beccf89064127baef7215f5891bbf 7656310 Encampment.savegame
410beccf89064127baef7215f5891bbf 7681832 CilantLs.savegame
410beccf89064127baef7215f5891bbf 7682189 CilantLs.savegame
410beccf89064127baef7215f5891bbf 7719700 CilantLs.savegame
410beccf89064127baef7215f5891bbf 7804695 GildedVale.savegame
410beccf89064127baef7215f5891bbf 7876020 TempleofEothas.savegame
410beccf89064127baef7215f5891bbf 7939096 TempleofEothas.savegame
410beccf89064127baef7215f5891bbf 7983987 Esternwood.savegame
410beccf89064127baef7215f5891bbf 10039971 StormwallGorge.savegame
410beccf89064127baef7215f5891bbf 10040293 StormwallGorge.savegame
There is also a folder within called 2.0 Save Games Backup, but it is empty.
You can see some manual saves in there. If I overwrite them in PoE, they disappear in the directory. Perhaps there's another location where things are going accidentally?
Any other ideas?