This is still an open question – at this moment, it appears that simple updates for MyEclipse are not working.
Actually, I just updated a test 4.0.1 install to 4.0.2 without any issue. I selected the main Eclipse.org update site (you should too) for the Eclipse.org mirror, and waited for it to be checked. Since we do all the mirroring of the MyEclipse update sites through dns aliasing, there won’t be a prompt for a MyEclipse update site mirror. Once the Eclipse site was searched and no updates were found, the next dialog page shows the MyEclipse update site that when expanded showed release 4.0.2. I checked the box, hit finish, and restarted and the upgrade went fine.
Can you check Help > Software Updates > Manage Configuration and expand the location of MyEclipse in the dialog. How is the product listed? Does it say MyEclipse Enterprise Workbench 4.0.1? Do any other versions show they’re installed as well? If it shows 4.0.1, what happens when you select “Scan for Updates” in the pane to the right?