EAGLE: can't delete wire in tDocu layer
Whenever you modify a package or symbol that is already in use in a board or schematic, you have to update the library so that the changes will take place on your current design (Library > Update... / Update all):



Depending on the changes you made, Eagle will suggest you to run DRC/ERC due to the modifications. 

You can update the specific library you modified, but I usually use "Update all" cause it is faster.