Hello,
I did a little experiment and found that there is a flaw indeed.
My model contains 2 packages with 1 class each, and an association drawn in the diagram in Package2 from Class2 to Class1 (which resides in Package1).
Now if I export each package to an XMI file (default options, i.e. XMI 1.3., enable full round trip, save diagrams a.s.o.), EA saves the association in both files, and puts the object which the orphan association end points to into an "EAStub" tag in the "XMI.extensions" branch. If I reimport both packages into another eap file, the association is duly being restored.
The flaw however is this:
If I reimport Package1 and then Package2, the result is excactly like my original model. If I do it vice versa, Class1 is missing in the Package2 diagram.
This means that when you have a complex model with various links across packages, the "source" (or the first association end, which is, of course, arbitrary in case of associations between classes, depending only on the direction in which you drag it on the diagram) being sometimes in one package and sometimes in another one, there is no way to restore the full project. The logical model will not suffer, but the diagrams will not be completely restored.
For the time being this means: A package which contains diagrams for objects from different subpackages must be exported and imported (or put under version control) as a whole unless you want to redraw those diagrams over and over again.
Frank