Are you talking about the FSDT_ZurichX folder in appdata because the FSDT_LSZH folder doesn't exist after uninstalling ZurichX...
The one under the FSX\Simobject folder.
The one under %APPDATA% it's always empty and doesn't matter (it's created by FSX itself).
It's normal you wouldn't see that folder anymore under the FSX\Simobject folder, because the uninstaller removes it, mine was just an EXTRA precaution to be entirely and absolutely sure you were starting from a clean situation.
But as I've said, I really don't have an explanation why the patch is not successful. It's not that is not running correctly, because it is, it's just that it reports your objects were EITHER already patched (but you shouldn't see any flickering in that case), or they are not as they are supposed to be in the current version of the installer, so they are not patched for that reason.
Would you like to try a Teamviewer connection, so I can have a look at your system ? PM me to arrange that.