The biggest problem you'll likely have is that 3.5 does not enforce
J2EE standards, particularly in packaging. If you already build and deploy as jar-in-war-in-ear with appropriate deployment descriptors, you're in good shape. However, I'd bet money that if you're on WAS 3.5 you aren't doing this and your dependencies are a veritible hodge-podge of evolution... leaving you in for a rough ride.
BTDT. Good Luck...