What are the best practices for handling custom security during Peoplesoft Upgrade?

We are currently working on a PeopleTools upgrade, and as part of the process, we need to import the PPLTLS84CUR project. During the comparison, we noticed a few issues: apart from some code being overridden, several delivered components are losing our custom Permission Lists.

While code changes can be preserved by copying objects into a custom project, we are looking for the best way to manage and retain security configurations, especially custom Permission Lists, during this process.

Has anyone faced a similar situation? What are the recommended approaches or best practices to handle this efficiently? Any tools, scripts, or automation tips would be greatly appreciated.