Folders disappear after mac os upgrades

I have a folder in the root of my system disk containing some large files (it is a vmware virtual machine), the folder is excluded in my Timemachine backup. In every mac os upgrade, for example from sierra to high sierra and even minor upgrades for example from 10.13.0 to 10.13.1 this folder disappears completely. The diskspace is also released so the folder is really gone.

I guess it is related to the fact that I have the folder excluded in Timemachine, but why is this happening?