Uploaded PDFs are always broken

Hi there,
I was trying to backup all the files via Filezilla by downloading them but whenever I upload it up everything seems to be working besides PDFs, some cannot be opened, some only display very limited information (1 word or logo only) but all of them are broken.
I read only that you have to upload them in binary and another user mentioned that all his woes are gone after setting Filezilla to auto, unfortunately I was already on auto and even changing to binary nothing changed.

Any ideas what could be the issue?

Best regards