When wyUpdate starts your app after an update, it uses the location of the wyUpdate.exe as the working folder.
We could add the ability to save the working folder location before the automatic update is installed. But this seems unnecessary.
Are you loading application resources or DLLs using the working folder? If so, that's not advisable. If you want to load resources relative to your exe use:
Path.GetDirectoryName(Application.ExecutablePath)
Tell me if this helps.