First make a Filter for all skills you wish to delete.
Filters | Add Filter | give the Filter a name and Save.
On the Volunteer Limits tab, scroll down to Skills.
Click the Edit Limitation button below and choose each of the skills you wish to delete.
You should see a double check>> to the left of each.
Scroll down on your Filter to Include Terminated Volunteers = Yes.
Run the Volunteer Skills report and set this Filter.
This will identify the volunteers with skills that you want to delete.
Once the skill you want to delete is no longer attached to the volunteer, you can delete it.
Reports | Volunteers | Volunteer Skills
Once you reassign the obsolete skills to a valid skill, you can then delete the no longer desired skills from the Skills list in preferences.