You added a system again, which was deleted from the LMDB and SMSY, to the SAP Solution Manager SLD using the transaction RZ70. The updated data is visible in the SLD but not in the LMDB.
LMDB synchronization job, processes the changes in the SLD only after the "full automatic synchronization" phase has been passed. No data is synchronized if there are no changes in the SLD.
Delete or restore the system in SLD as well.
For more information on restoring a deleted system, refer to http://service.sap.com/solutionmanager -> Media Library -> Technical Information.