Hi Erin
I tried some workarounds for your first question such as hiding competencies and looking at permissions for this but I couldn't get the competencies to have separate access for roles. Possibly you could allow the learner to choose competencies for core company competencies and the manager could delete inappropriate ones.
For the second question the competency does stay in the state it was when a learning plan that includes the competency is deleted. I think this is the expected behaviour - if you have achieved a level of competency then you should retain this.
regards