Update Office from 2011 to 2016

Are you targeting the Office 2011 activation file in the clean up script? If so, are you targeting it directly or doing a blanket removal of any com.microsoft.* files in the /Library/Preferences directory?

I think we have figured it out.
MS Office 2011 license file is /Library/Preferences/com.microsoft.licensing.plist
MS Office 2011 license file is /Library/Preferences/com.microsoftV2.licensing.plist

Our sequence of action for testing was as follows.

1. Install Ms Office 2011

2. Install Ms Office 2016
   This will update the Office 2011 licensing file to Office 2016 license file and there will be no two licensing files in /Library/Preferences/

3. Remove Ms Office 2011

The script had syntax rm -R /Library/Preferences/com.microsoft.licensing*.plist
which was also removing Ms Office 2016 license file and was causing license information completely missing from the Mac OSX.

We changed the script line from
/Library/Preferences/com.microsoft.licensing*.plist
to
/Library/Preferences/com.microsoft.licensing.plist

This is the remove Office 2011 script I use based on one from OfficeforMacHelp. As you have noted, you must specify that licensing.plist, otherwise you may knock out the 2016 licensing plist file too, if you installed that version before removing 2011.

Ideally, you want to remove 2011 first, then install 2016. This script will leave behind the "Microsoft User Data" folder in the user's Documents folder, so it'll be easy to import the Outlook data into the new version. After the data is imported, you can delete the "Microsoft User Data" folder.

#!/bin/sh
    osascript -e 'tell application "Microsoft Database Daemon" to quit'
    osascript -e 'tell application "Microsoft AU Daemon" to quit'
    osascript -e 'tell application "Office365Service" to quit'
    rm -R '/Applications/Microsoft Communicator.app/'
    rm -R '/Applications/Microsoft Messenger.app/'
    rm -R '/Applications/Microsoft Office 2011/'
    rm -R '/Applications/Remote Desktop Connection.app/'
    rm -R '/Library/Application Support/Microsoft/MAU2.0'
    rm -R '/Library/Application Support/Microsoft/MERP2.0'
    rm -R /Library/Automator/*Excel*
    rm -R /Library/Automator/*Office*
    rm -R /Library/Automator/*Outlook*
    rm -R /Library/Automator/*PowerPoint*
    rm -R /Library/Automator/*Word*
    rm -R /Library/Automator/*Workbook*
    rm -R '/Library/Automator/Get Parent Presentations of Slides.action'
    rm -R '/Library/Automator/Set Document Settings.action'
    rm -R /Library/Fonts/Microsoft/
    rm -R /Library/Internet Plug-Ins/SharePoint*
    rm -R /Library/LaunchDaemons/com.microsoft.*
    rm -R '/Library/Preferences/com.microsoft.office.licensing.plist'
    rm -R /Library/PrivilegedHelperTools/com.microsoft.*
    OFFICERECEIPTS=$(pkgutil --pkgs=com.microsoft.office.*)
    for ARECEIPT in $OFFICERECEIPTS
    do
        pkgutil --forget $ARECEIPT
    done
exit 0

We have had office 2016 crash so much that we rolled back to office 2011, I hope it works out for you.

Thats why I am insisting on first removing O2011 and then install O2016 but thats not my decision. The requirement is to coexist both Offices to minimize down time and then remive O2011 once O2016 has been installed. However, Office 2016 we have installed at the start of this year on fresh new machines has been going on OK for the last three months whereas upgrade was never tried before. @anickless did you had issues while upgrading other than licensing issues. I think Composer might help identifying the dir structure for both Offices and then update the 2011 uninstall script accordingly.