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.