Here is the scenario - machine is already encrypted fully by an install set that was created with the 5.1.6 Device Encryption files. Another install set was created taking into account the 5.1.8 client files. The installation runs successfully over the top of the "old" build (eepc.exe) however after a reboot, looking in the Client Status window - it is just blank. Even hitting sync doesn't bring anything else up.
Funnily enough I got the same problem when I pushed the files down from the console as well. Reason for the 'reinstall' as it were is because it has already got an entire set of users on the machine and the new job uses the autodomain script during install
An upgrade won't remove your users. It just replaces the associated fileset. When we went from 5.1.3 to 5.1.7, we kept the C:\Program Files\SafeBoot path on new installs. Existing installs should continue using [APPDIR] which was defined during their original install. Installing over the top of an existing install is only asking for trouble. At the next synch, it will likely undo what you tried to do with the reinstall. It would probably also fail to update files that are in use and not properly upgrade the SBFS files.
It sounds like you should call for a support person or installation assistance. I believe that your misinterpretations of how the system operates could cost your users dearly.