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Check if there are any temp files in <Endeca_Instance>/Workbench/workspace/state/emanager/instances/<app_name>/resources/locks. if there are any files try logging in and break all the locks from Workbench --> Application Settings --> Resource Locks
Also check the error in [ENDECA_CONF]/logs/shell/<app_name>.emgr_update_update_mgr_settings.log
This error is basically because of the version mis-match for the packages that are being installed.
Try installing the correct packages that is compatible with the same. For the compatibility check have a look at the compatibility matrix for your MDEX version.
Ex: Compatibility matrix for MDEX 6.2.2
Thanks & Regards,