You should be able to open Authorization Manager, log in, enter the new serial number and click OK/Next. After that, you can open Custom Shop (in your Start Menu on Windows, Applications folder on Mac) and then log on there, go to AmpliTube --> Gear --> Restore My Gear to make 100% sure that all gets set correctly and you should be all set.
If this doesn't work for you, please open a ticket with IK Support at
http://www.ikmultimedia.com/contact-support and they will troubleshoot and assist you directly.