Dear Antony,
If the old universe are upgraded from previous version (eg: from R2 to 3.1)
You should not remove the contents in the old universe and then build some new objects in this universe. It will create some unexpected bugs.
You should rebuild a new universe from the beginning.
If the old universe are not upgraded, you can remove the contents in the old universe and then build some new objects in this universe so that we can keep the access restriction.
Thanks & Regards,
Gordon