Hello, sorry for the question, but in which folder did you put back the save and hi-scores?
It seems that while previously hi-scores were in recalbox\saves\fba_libretro\fba
, now it saves and loads from the recalbox\saves\fba_libretro\fbneo
folder, due to the fact the core changed name.
Also the states seems to be directly in recalbox\saves\fba_libretro
Maybe it's the reason, though I am not sure about the states.
EDIT: I assumed you were using the fba_libretro folder, if you are using the neogeo one, I am not sure if it has the same principle, but that may be worth looking into.