will this take effect if I trigger it calling a powershell script with maxscript, and thus take effect instantly, or will max need to be closed, in which case I need to think of a logon script perhaps that set the path...
It takes effect only the next time that Update Manager is launched, and dowloads the libraries to the new location.
When this take place, the following registry keys are also updated, which defines the location of the assets for each plugin:
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\Forest Pack Pro\EffectsDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\Forest Pack Pro\LibraryDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\Forest Pack Pro\MatlibDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\Forest Pack Pro\TexturePaths]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\RailClone Pro\LibraryDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\RailClone Pro\MacroDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\RailClone Pro\MatlibDir]
[HKEY_CURRENT_USER\SOFTWARE\Itoo Software\RailClone Pro\TexturePaths]
So, if you want to define the library paths using the registry, i would suggest to set these keys as well. They must be assigned before plugins are loaded in Max.
If needed, you also can run Update Manager by command line. Use "C:\Program Files\Itoo Software\Common>UpdateManager.exe help" to see the parameters.