I had the same problem the domain objects are scattered into multiple java projects, These projects intrun are part of an ear file. Since all the domain objects and mappings are in individual jar file when I start the application I got the same error as you described in your post.
I resolved the problem by adding class definition of all domain objects into the persistence.xml file
1. Poject A -- projecta.domain.One
2. Project B -- projectb.domain.Two
<?xml version="1.0" encoding="ISO-8859-1" ?>