2125656 - AS Java fails to start due to Safe Mode

After an installation or upgrade operation done by a supported tool (e.g. SUM, SWPM, etc), the AS Java instance does not start anymore. In SAP MMC you can see that it is stuck on the Bootstrap phase, and in the dev_jstart log there is an entry as below:

F [Thr 01] *** CONFIG => instance is disabled.
F [Thr 01] *** LOG => Run level 3 completed.
F [Thr 01] *** LOG => Instance state is "Synchronizing binaries" (STOPPED @ 0, INACTIVE).

In the jvm_bootstrap.out log there are entries as below:

Safe mode lock imposed by instance [ID65848]; local instance will be disabled

Instance [ID14679] will run in [SAFE] mode; performing action [DEPLOY]

SAP NetWeaver Application Server Java

safe, mode, deploy, bootstrap , KBA , BC-UPG-TLS-TLJ , Upgrade tools for Java , BC-JAS-COR , Enterprise Runtime, Core J2EE Framework , BC-INS , Installation Tools (SAP Note 1669327) , BC-UPG-OCS-SPJ , Please use component BC-UPG-TLS-TLJ , Problem