On HiveManager 6.1r3. Had IP Policies setup and working. Not sure if it was the system update, however the IP Policies are now missing. I do not know when they went missing. It is not something I check regularly.
First off, if you do not have a backup, you will need to recreate whatever is missing.
Do you self-host HiveManager or make use of HiveManager Online (HMOL)?
Which version are you using now? Your first sentence is ambiguous. Do you mean that you were on HiveManager 6.1r3, or that you are now on 6.1r3?
(If you were using HMOL 6.1r3, you should not have been moved to HMOL
6.1r5 unless you explicitly requested it or purchased HiveAP 230s.)
It is more likely that this is something that has been changed accidentally or intentionally by an administrator of your HMOL instance rather than a change introduced by an update process. Have you checked the logs to see if somebody made such a change?
If the logs do not show this, you should consider opening a support case with your point of support to investigate further.