If the overall apply RC was 4, the the IEW2646W messages can be ignored. Linkage editor messages IEW0461, IEW2454, IEW2646, IEW2651, and IEW2689 are produced during the APPLY stage for unresolved external references. These are issued, giving a return code of 4, when some load modules are link-edited during PTF installation.
You can ignore these IEWxxxx messages because they are produced for component object modules of executable load modules.