Only “Configure your relays…” and “Announce your relays..." can mess up your relay settings
Configure... is on device and can sync via iCloud, doesn’t mess with other apps, only Nostur.
Announce… is published on relays and can mess with other apps that read relay configuration from nostr relays.
Autopilot is in memory and doesn’t change any settings, you can turn it on or off and your relay configuration will be intact.