2689514 - Java Instance fails to start after performing a System Copy

When trying to start the Application Server Java you receive this error on the dev_bootstrap file:

F ********************************************************************************
F *** ERROR => Node 'bootstrap' failed with exit code 513.
F ***
F *** Please see section 'Failures in the 'synchronizing binaries' phase'
F *** in SAP Note 1316652 for additional information and trouble shooting advice.
F ********************************************************************************

...or:

F ********************************************************************************
F *** ERROR => Java node 'Instance_bootstrap' terminated with exit code 549.
F ***
F *** Please see section 'Java program exit codes'
F *** in SAP Note 1316652 for additional information and trouble shooting advice.
F ********************************************************************************

And inside jvm_bootstrap.out:

----------==[ Caused by: ]==----------
com.sap.engine.lib.config.api.exceptions.NameNotFoundException: The specified identifier ID6367969 is not valid for level [instance].
at com.sap.engine.lib.config.impl.CommonClusterFactoryImpl.openConfigurationLevel(CommonClusterFactoryImpl.java:107)
at com.sap.engine.bootstrap.StorageAccess.getConfigurationLevel(StorageAccess.java:744)
at com.sap.engine.bootstrap.SynchronizationInfoImpl.getInstanceData(SynchronizationInfoImpl.java:617)
at com.sap.engine.bootstrap.SynchronizationInfoImpl.collectSynchronizationData(SynchronizationInfoImpl.java:169)
at com.sap.engine.bootstrap.Bootstrap.main(Bootstrap.java:301)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.sap.engine.offline.OfflineToolStart.main(OfflineToolStart.java:162)
Caused by: com.sap.engine.frame.core.configuration.NameNotFoundException: Configuration [ID6367969] not found in [cluster_config/system/instances]

SAP NetWeaver Application Server Java

com.sap.engine.frame.core.configuration.NameNotFoundException: Configuration exitcode 513 exitcode 515 exitcode 549 swpm system copy exit code java startup bootstrap , KBA , BC-INS-SWPM , Installation with Software Provisioning Manager , BC-JAS-COR , Enterprise Runtime, Core J2EE Framework , BC-INS-MIG , OS/DB Migrations with SWPM and DB refresh , Problem