I've actually had the EXACT same problem with the last 4 or 5 updates I've done.

After the update %ZENWORKS_HOME%\conf is seen by ZDC. I can set it to EVERYONE and run ZDC and it's fine. I have a LOT of \downloads\MSI files missing, and a LOT of \lib\Java files missing.

I'm still working on a duplicate server that I can upgrade and copy the files from and hopefully that'll fix it like it has the last few times, but what in the world is causing this?

It is attached to domain, but I have blocked GPOs from that OU except for WSUS server.

Windows Server 2008R2 VM
Embedded Sybase
ZCM 11.3a to 11.3.1