Hello.
I just had a similar problem, but in my case I caused it.
I'm selling my exploitable, or exploited, Ps4 slim, I need the money for payments. I made a backup with the backup option in al azif self hosted exploit.
When I was gonna delete my backups to leave the console clean, the buyer backed, so I just deleted the save data.
Trying to have it back I copied the contents through ps4 explorer and broke the data base, which got rebuilt after a restart and I lost the games and homebrew I had installed.
The system still recognizes space used, same I had before. So i re installed the fpkg of file explorer, the console told me it was already installed, through it I copied over my .db backups and boila!
Now I have the games again. Savedata is gone though.
So if you don't have that backup you will need to re installed the games again.
I just had a similar problem, but in my case I caused it.
I'm selling my exploitable, or exploited, Ps4 slim, I need the money for payments. I made a backup with the backup option in al azif self hosted exploit.
When I was gonna delete my backups to leave the console clean, the buyer backed, so I just deleted the save data.
Trying to have it back I copied the contents through ps4 explorer and broke the data base, which got rebuilt after a restart and I lost the games and homebrew I had installed.
The system still recognizes space used, same I had before. So i re installed the fpkg of file explorer, the console told me it was already installed, through it I copied over my .db backups and boila!
Now I have the games again. Savedata is gone though.
So if you don't have that backup you will need to re installed the games again.