This causes significant issues e.g. the beacon loads an outdated configuration looking into an outdated path, if existing at all. What can be done to prevent the change to the BaseDirectory value?
This behavior is caused by a known issue. When an inventory beacon perform a silent upgrade it will automatically revert to the default install directory. The only current workaround for this issue is to manually modify the changed registry keys following the install. This issue can be tracked through reference FNMS-29295