I will not helping a lot but I have same kind of issue:
Filesystem Size Used Available Use% Mounted on
/dev/mmcblk0p3 114.9G 110.7G 0 100% /recalbox/share
It seems that it's happening when I remove files from WinSCP or Putty for exemple (I find it easier when I have to remove a directory like in Dosbox emulator)
I have searched on the web for refreshing this lost free space but everithing I can find is tutorials on how to find the dummy/trash/lost files...
Not a big deal because I can still copying games on the card, but updates are crashing because of the "lack" of free space