However we can't do that for >1000 machines over >100 sites, so I need to find some way to script this. However I tried a manual repair from Control Panel\Programs and Features and this worked correctly and fixed the issue.

Setup.exe /repair ProPlusWW but it said that the install was corrupt and I'd have to use the msi. I've tried running c:\program files (x86)\common files\Microsoft shared\office16\office setup controller\ (that I know of, unless the install leaves it in a folder somewhere). It looks like I need to do a quick repair on the Office install, but a) it needs to be silent and b) the install msi isn't on the machines to use for the repair. Script that runs immediately post upgrade. I need to find a way to add a fix to the PowerShell

Unfortunately the upgrade from Windto 1709 breaks Outlook search - presumably the indexing. We have Windows 10 systems running Office 2016 ProPlus installed from the msi during the build from SCCM. I've posted this on the Office forums but they directed me here.