Hey Brent,
It stores just those settings that are changed from the defaults. The problem is that this information gets lost in the update. I know that, for example, the ClickOnce updater imports settings from previous versions, but the AutomaticUpdater doesn't know to do this ... unless I am missing something.
Is there a way to avoid losing this config information during the update?
Unfortunately the AutomaticUpdater doesn't do this by default. It's a good idea. I'll see if we can squeeze it in for the wyBuild 2.6 release. It might come in 2.6.1 or 2.6.2.
Though there is a hacky way you can do this with the current version:
Use the "ReadyToBeInstalled" event to save the current config location to registry and then use the "UpdateSuccessful" event to copy over the old config information to the new location.