In ccleaner -> advanced options you can define, that only files in windows temp folder being older then 24 hours are to be deleted.
I really wish this would be extended to Custom "Folders and Files" because I cleanup files in some upload folder and I don't want to delete files with ccleaner that are currently in use.
...Then untick 'Custom Files and Folders' when you don't want to use it, or 'Exclude' wanted folders or files from being deleted.
It's actually odd to add your Upload folder to 'Custom Files and Folders' since there's going to be needed files in it, you could just manually manage that Upload folders contents.