Apple Pay Suica is different from Apple Pay credit cards in that your Suica can only exist on a single device. Apple Pay credit cards can coexist on iPhone, Apple Watch or iPad, not so with Suica.
When you migrate to a new iPhone or Apple Watch you have to remove Suica from your old device first before setting up your new iPhone. Fortunately this is very easy to do. In Wallet simply delete Suica from the old device before migrating. Once you have setup your new iPhone simply add Suica in Wallet in the new device as shown in the above video. JR East has a nice Japanese support video too showing the same operation.
Don’t worry about losing your Suica SF account balance or commuter pass information. Apple Pay and the Mobile Suica system preserve all of your Suica information. Just make sure that you are signed in with the same Apple ID on your new iPhone and that Apple Pay is turned on.
New iOS 11 Apple Pay Suica reminders
In iOS 11 you should notice two new reminder options in Suica Wallet. For all Suica users there is a charge reminder you can set once your Suica balance falls below your chosen limit. For Suica commuter pass users there is a commuter pass reminder you can set so you will not miss the two-week pass renewal window.
Update: Make sure that you delete Suica before setting up your new iPhone.