Hi,
we have no clue what steps did you take in Cleanup, could you please specify that?
I guess it could be caused by deleting of residuals by Safe Clean. Sometimes users use some app e.g. Whatsapp that downloads a lots of photos, then they uninstall Whatsapp and use Safe Clean. In that moment those photos and other files gathered by Whatsapp are considered "residual files" and in default setting of Safe Clean they are deleted. Could it be your case?
Let us know please.