iCloud doesn't show files I have recently uploaded

Hello,

I have recently cleaned my drive and reinstalled Mac OS on my Macbook Pro. Before doing so, I uploaded all the files I wanted to be backed up and saved. After I reinstalled the OS, I enabled iCloud and it started downloading the back up folders. However, most of the folders are empty of context and it seems broken and most of the big files are missing! 90% of the data I have is now missing or not downloading! What do I do?

Thanks.