This is how I update Adobe Reader (and many other products), so I can speak to this out of some experience.
When I need to deploy an upgrade to Adobe Reader (or other packages), I do so as follows:
- Stage the new version of Adobe Reader in my domain DFS software distribution share.
- Perform a test silent installation as SYSTEM onto a test client computer and verify functionality.
- Add the new Adobe Reader to the existing GPO where Adobe Reader is installed, marking it as a mandatory upgrade for the existing verison of Adobe Reader, selecting "Uninstall the existing package, then install the upgrade package" when I Do so.
- Modify the permissions on the assignment of the new Adobe Reader package to constrain deployment to a single test computer.
- Boot the test computer and verify removal of the old and installation of the new. Logon and test for functionality.
- When I'm satisfied that the testing is successful, modify the permission on the software assignment for the new Adobe Reader to allow distribution to all intended client computers.
Computers that already have Adober Reader 9.1.0 will uninstall the old version and install the new version. Computers that don't have Adobe Reader at all will only install the 9.1.2 version.
Later, then 9.1.3 (or whatever) comes out, I'll do the same thing again. If I'm sure that all my old 9.1.0's are gone I can go ahead and remove 9.1.0 from the GPO, but I should be sure that they're all gone before I do that.
Technically, it is possible to apply MSP patches to installation points (such as the Adobe Reader 9.1.2 MSP, which can apply to Adobe Reader 9.1.0 installation points) and "Redeploy" the package. I've done this with Microsoft Office in the past, but anymore I'm just deploying a new package as an upgrade to the old. The only time I would do this "patching the install point" today is if only an MSP were provided by the vendor.
Don't do the upgrade in another GPO-- do it in the same GPO where you assigned the software to begin with. Then you don't have to have any anxiety about "link order". (You really shouldn't have anxiety about "link order" anyway. Sit down and have a good long look at how Group Policy builds the list of policy objects and applies them, and it will make sense. All this hooey about "precedence" in Group Policy in current Microsoft operating systems is just confusing. It's all just building a list of GPOs starting at the site, then the domain, and then working down to the computer or user object, and then applying that list in the order that they are found. I don't know why technical writers have to try and make it overly complicated... >sigh<)
When you say "...so it shouldn't have to transmit the full package", I believe that you're speculating that, because the clients already have some version of Adobe Reader, the installation of the newer version will cause less data to be moved over the wire. This would only be the case if the Adobe Reader 9.1.2 MSI were written to do so. Typically, I don't care how much data moves across the wire and I'm loathe to trust the MSI to do the right thing, so I nearly always choose the "Uninstall the existing package, then install the upgrade package" option.