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 must delete Suica from the old device first before setting up your new iPhone. 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 set the Region to Japan and 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. After Suica is back in Wallet on the new iPhone you can change the Region setting to your preference.