It happened again some weeks ago when I installed the Connections 220.127.116.11 fixpack, all the users I added to the security roles of the different apps were gone after the update 🙁
But instead of adding them again manually through the Admin console I searched for a better solution and found an old blog entry from Marco Ensing:
This was the basis for this little jython script, which you can use to recreate your settings:
Just download it & open it with a text editor. It’s rather self-explaining, add your users and change roles where needed.
Finally run the script via wsadmin tool:
wsadmin.bat -lang jython -port 8879 -username wasadmin -pw YOURPW -f ConfigureConnectionsRoles.py