I also faced the same issue. Identified that all the access point which is not registering into WLC is connected to same switch(3850). I physically changed the connectivity to another switch. After that it is automatically registering into WLC. So I ...

 Switch(Config)#no switch 2 provision ws-c3750-48tsSwitch(Config)#no switch 3 provision ws-c3750-48tsSwitch(Config)#no switch 4 provision ws-c3750-48tsSwitch(Config)#no switch 5 provision ws-c3750-48tsSwitch(Config)#wr memSwitch(Config)# Reload

 Switch(Config)#no switch 2 provision c9300-48uxmSwitch(Config)#no switch 3 provision c9300-48uxmSwitch(Config)#no switch 4 provision c9300-48uxmSwitch(Config)#no switch 5 provision c9300-48uxmSwitch(Config)#wr memSwitch(Config)# Reload