You should believe that the VMware Update Manager was capable of handling missing files. But no, it does not. I removed a couple of files from the repository by simply pressing delete on them. These files were part of a host upgrade baseline and were no longer needed.

After the delete operation, I can no longer scan the hosts successfully. The scan failes with “invalid state” even though the event list says the scan was successful. After tried restarting the update manager service and vCenter, I guess the next step is a full reinstall since I do not like poking around in the database..