The CLEANUP command

The CLEANUP command deletes entries from the SMPLTS, SMPMTS, SMPSTS, and SMPSCDS data sets. This is helpful for:

APPLY followed by ACCEPT when several target libraries have been created from the same distribution library: When a SYSMOD is accepted into a distribution zone, the entries associated with the SYSMOD are automatically deleted from the SMPMTS, SMPSTS, and SMPSCDS for the related target zone. However, even if the SYSMOD was also applied to other target zones created from the same distribution zone, these data sets for the other target zones are not cleaned up.
To delete the entries from these data sets, you can accept the SYSMOD and name these other target zones as the related zone. However, this updates the distribution library each time, which is time-consuming and can use up space in the distribution library data set. Instead, you can use the CLEANUP command, which deletes entries from the SMPMTS, SMPSTS, and SMPSCDS without updating the distribution library.
ACCEPT followed by APPLY: When a SYSMOD is applied after it has been accepted, the entries associated with it are not deleted from the SMPMTS, SMPSTS, and SMPSCDS. To delete these entries, you can use the CLEANUP command.
UPGRADE: When the UPGRADE command has been run to create an UPGLEVEL subentry for a zone, the SMPLTS data set for that zone does not need to retain a load module or program object unless it has both CALLLIBS and XZMOD subentries. You can use the CLEANUP command on the SMPLTS data set for a newly upgraded zone to delete from it any no longer needed load modules or program objects. You only need to run the CLEANUP command against an existing SMPLTS once, when its zone is first upgraded. Thereafter, SMP/E will no longer create unneeded load modules or program objects in it. You will never need to run the CLEANUP command (for this purpose) for an SMPLTS for a zone newly created with an UPGLEVEL subentry.