Hello,
you should have a central executable directory, which is configured in the parameter DIR_CT_RUN, you should exchange the kernel executables only in this directory and just restart the whole system. In the profiles the start of sapcpe should be configured, sapcpe will copy the executables from DIR_CT_RUN directory to the local executable directories of the instances (configured in the parameter DIR_EXECUTABLE). In sapcpe.log you can check, if all executables were copied succesfully. If it is a system running on a unix server you may need to check executables, which have root as owner, if the files were copied and if the files have still root as owner.
regards,
Alwina