client.wyc vanishing after installing

I have several wybuild projects used to patch my application's 4 possible configurations. My windows installer installs one of 4 client.wyc files depending on the choices made during setup. We've decided to change from patching to a full download using the wyupdater. In the meantime, I've changed all the wybuild projects to pick up the setup.exe and install from new.

If the windows installer is run without using wyupdater, it throws an error if a previous version is installed. The user must uninstall the original and try again. This is good.If wyupdater is used:If the user runs the windows installer and selects the same configuration as the previous, the update works fine.If the user changes the configuration then the client.wyc isn't installed and wyupdater throws an error that it couldn't find the client.wyc file. I don't know how wyupdater works but it looks as though the old application wasn't uninstalled, or my setup.exe isnt delivering the client.wyc file. I've no clue how to fix this.Anybody able to help please?