Go into the editor and create a new file.
If you want to remove the skill under all circumstances, go to the *Hidden tab - add a new entry, and enter the Id of the skill (to get that Id, go to the skills tab, press new (copy), and find that skill in the list - write down the part that's in parentheses).
If you want to remove the skill only while a specific option is enabled among the configure hero options, first, you'll need the Id of that option.
In the main HL window, go to the develop menu and make sure that the first option, "Enable Data File Debugging" is enabled. Now, in the Develop menu, select "Floating Info Windows" and then "Show Investigator Tags" - scroll down in that list to the set of entries named "Source Volume", and identify the one you want to work with (you can turn it on and off in Configure Hero, looking back at the list each time, if that helps you figure out which one it is).
Okay, now back to the editor - in your open file, go to the *Preclude tab, create a new entry, enter the skill's Id and enter the source's Id.
Option 3: You want to replace the skill with a different one. Go to the skills tab, press "New (Copy)" - once you find the skill you want to replace in that list, write down the unique Id of that skill, then select it. Enter the unique Id in the "Replaces Thing Id" box on the middle-right of the screen, and modify the rest of the skill as you wish.