no, they're definitely gone.
strangely, my cheat files are still there
i had my record super metroid time in there too
my path.ini:
usePathINI=1
E:\zsnexbox\bookmarks\
E:\zsnexbox\artwork\Shots 1\
E:\zsnexbox\artwork\Shots 2\
E:\zsnexbox\artwork\Shots 3\
E:\zsnexbox\artwork\Shots 4\
E:\zsnexbox\artwork\Shots 5\
E:\zsnexbox\artwork\Shots 6\
E:\zsnexbox\artwork\Shots 7\
E:\zsnexbox\artwork\Shots 8\
E:\zsnexbox\sram\
E:\zsnexbox\save\
E:\zsnexbox\ini\
E:\zsnexbox\rumble\
E:\zsnexbox\cheats\
E:\zsnexbox\garbage\
F:\emulators\xsnes9x\roms\
Do you have less than 1.2 GB free on your E partition? If so, phantom file/folder deletions/coruptions are possible (it's happened to me).