Ames (Urbit's networking protocol) has the unique property of "exactly-once messaging", meaning it guarantees a message sent to another ship will be delivered once, and once only. This property is highly desirable and greatly simplifies writing networked applications, but it requires that the ordering and receipt of every single message to every ship is carefully tracked by Ames.
When an older copy of a ship is booted, it will not know about the newer messages it has sent and received, so will be out of sync with the remote ships it's communicating with. The remote ships will not resend messages they know to have already been delivered, your ship will reject their new messages because there will be a gap in the sequence, and the remote ship will refuse the messages you send because of reused message numbers. This situation cannot be fixed, and will create permanent networking issues with those ships. We therefore recommend you don't keep multiple copies of your pier lying around, and take great care to never boot an old copy if you do.
- Guide to Factory Resets: How to perform a factory reset through Bridge if you accidentally double-boot your ship.