If you want to exclude the file from updates, then remove it from the current version and the old versions. This way when wyUpdate updates your app it will just ignore the config file.
If you just remove it from the current version but leave it in the older version, then when wyBuild builds the updates it will read this as "there used to be a file, now there's not. wyUpdate should delete this file on update".
How do you deliver new config files?
Let's say your config file is named "YouApp.config" and it may or not may exist on your users' machines (depending on what version they're upgrading from). This means you want to distribute this file and use it as the default config for a user, but you don't want to overwrite the file if it already exists.
There are a few ways to do this. By far the easiest is to add the file as "YourApp-sample.config". Then, either on the first run of your app or as part of your update, copy the "-sample" file to "YourApp.config" if that file doesn't already exist.
Does this make sense?