I think I can hopefully clarify the example and maybe help show why this is incredibly confusing:
1. New workflow, File->Save Archive (kar1), Run. The report designer shows the report, the report viewer is a blank page, and kar1 has workflow_ROML.xml.
2. Bump LSID (I usually delete & undo), File->Save Archive (kar2), Run. workflow_ROML.xml is missing from kar2.
3. Close & reopen kar1, Run. The report designer is blank and the report viewer shows the report. I think this is bug 4571.
4. Bump LSID, File->Save Archive (kar3), Run. The report designer shows the report, the report viewer is a blank page, and kar3 has workflow_ROML.xml.
5. Now, if we export all the runs, the first is missing workflow_ROML.xml, the second has a minimal workflow_ROML.xml, the third has a minimal workflow_ROML.xml but the full ROML.#.xml, and the fourth has what I think is RIO.#.xml content in workflow_ROML.xml but a minimal ROML.#.XML and a minimal RIO.#.xml.
There is another test sequence:
1. New workflow, File->Save Archive (kar1), Run, Export run (run1). The report designer shows the report, the report viewer is a blank page, kar1 has workflow_ROML.xml, and run1 is missing workflow_ROML.xml.
2. Bump LSID (I usually delete & undo), File->Save Archive (kar2), Run, Export run (run2). kar2 has a minimal workflow_ROML.xml, and run2 is missing workflow_ROML.xml.
3. Close & reopen kar1, Run, Export run (run3). The report designer is blank and the report viewer shows the report. Bug 4571 again, but run3 has the full workflow_ROML.xml.
4. Bump LSID, File->Save Archive (kar3), Run, Export run (run4). The report designer shows the report, the report viewer is a blank page, kar3 has workflow_ROML.xml (with RIO.#.xml contents), and run4 is missing workflow_ROML.xml.
Right now, I think these examples show off some of the biggest problems in the way of being able to repeatedly change, save, and run, which is pretty central to building reports.