Sally- Uftree.exe (v2.x) and Uftree (v3.x) can coexist in the same computer in different directories, and can be installed in any order. But the Win Registry will point to the folder containing the Uftree.exe file last installed, either from the basic CD, or from a downloadable upgrade.
After the release of UFT 3.0, many users reverted to the UFT 2.8 downloadable upgrade (or a rare 2.9) because of bugs in UFT 3.0. This caused the Win Registry to point to the 2.8 version. Then, when the UFT 3.1 patch was released, it could not find the UFT 3.0 installation in the registry.
Solution: Install UFT 3.0 again, and then install the appropriate 3.1 patch.
As to a later installation of Roots having an effect on the UFT registry, probably not. I don't know.
As to the continued used of the UFT 2.x "Gateway", that may be problematic, depending on the install sequence. Thanks, Blue & all.