@Agharti,
You have created a skills library, with shortcuts from what I understand above. Then on the character sheet, you replace the shortcut with your library shortcut? Or are you deleting the skill from the character sheet and generating a new line with the library skill shortcut dropped onto the list?
I ask because I can see how/why basic skills built in from the rule set could overwrite the custom.
The idea is this: (first few skills from the basic list)
Awareness
Barter
Don't delete them, just make an entry in your skills library named the same and replace the shortcut on those lines. It won't overwrite. If the name is different, depending on what your or players are doing, issues may occur.