As long as the ALLWKST.EXE is current, you can use it for setting up new workstations.
You shouldn't need to run a workstation setup for computers that have used Adagio in the past. Adagio will automatically detect if one is needed when you start the program. The exception is in the scenario you ran into, where the program upgrade gets installed to a new location and shortcuts need to be assessed for the correct place.
When installing upgrades, it is always desirable to read the Readme or the release notes to see the important notes regarding things to be aware of when performing the upgrade.
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Regards,
Softrak Tech Support