Exile.cs is synced with the bot. As changes are made to the API or the CR itself, they have to be included in every version deployed. Since Exile is the generic CR we provide as an example, it's best to make your own copy with a different name to avoid the updates from wiping it out (also a good idea to keep backups of your CRs!)
Item filter is created by default when one does not exist. I'm not too sure of the updater behavior with it, but my strategy for using the bot is to keep each version in its own folder rather than one folder that is updated version to version. I think that is better for keeping track of things and avoids the issues that can happen when updating as the update process sometimes doesn't work and you need to download a fresh copy of the bot.