How to reset permissions
One answer
To remove any customization in a child project area, use the RTC Eclipse client and remove the appropriate section in the Process Configuration Source tab. For example, to reset the permissions, remove the <project-configuration><permissions>, and <team-configuration><permissions> sections. If you remove the entire content in Process Configuration Source of a child project area, the child project area will inherit all configurations of the parent project area.
Can you please elaborate that the child project area "had permissions customized before a master project area was applied"? It is recommended that the child/consumer project area is created from the Unconfigured Process template.
Comments
A little knowledge is a dangerous thing. A bunch of Lifecycle projects were set up before I was hired using the Scrum template and placed in use. They didn't know about master project areas. Some project areas requested individual customizations. Then, since this really isn't an Agile Scrum program as it has a formal System Integration Test team and contractual requirements, I was asked to make some changes to the Defect record as well as adding some roles so only the test team could 'pass' or 'fail' Stories & Defects. I used a master project area to implement this and then pointed the existing projects at it. As you might imagine there were side effects.