From atadistance:
The Apple Pay ‘ka-ching’ sound and ‘Done’ mark do not mean Suica Recharge is completed. Check card status: when the Updating Cards alert disappears and the Balance updates, Suica is ready to go. If the recharge process seems stuck because of a poor network connection simple cancel and try again when you have a better connection.
Have you tried just reloading again? Make it a nominal amount just to see if it will go through.