You can't edit the things in the source directory directly. You create a new file within the editor, and create your new items in that.
What unique ID did you give your skill?
Did you delete the skill from the srd_skills.dat file in the source folder? Every file in the source folder is there as a reference. They are not used for the actual data. The thread I mentioned describes the basics of how to use the hidden mechanism (although that mechanism is not available from within the editor - you'll have to edit the XML directly)
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