So you can open smaller sized zip files but not the larger ones it appears.
Do you have any Mac computers that are NOT running El Capitan? If so what happens if you upload a large zip file using that computer? Can the zip file be opened? What you need to do is isolate what exactly is causing the problem, is it the El Capitan OS itself? Or is there some other cause.
If El Capitan is corrupting the large zip files as its being copied there is, in all likelihood, nothing that can be done to fix the corrupted zip file. You’d probably have to use a Mac OS other than El Capitan to zip and upload the files to the My Cloud if you have to use zip files.
It is easy to blame WD’s My Cloud in this instance but there are certain issues that Apple’s El Capitan introduced that are causing problems with the interaction between El Capitan and the My Cloud. In some of those cases its the fault of the Apple OS and not necessarily the fault of the My Cloud. There is a big El Capitan thread at the following link where there is much discussion on El Capitan issues and some potential solutions or workarounds (probably not for your issue however):
https://community.wd.com/t/support-os-x-el-capitan/96744
