3699125 - SAP Java system startup failure due to synchronization binaries issue

• SAP Java system fails to start, displaying the error message: "Node 'bootstrap' failed with exit code 556. 
  
  
• Watchdog timeout occurs, initiating a full thread dump due to no progress recorded since a specific timestamp.
  
  
• Error while deleting native file: "/usr/sap/<SID>/J00/j2ee/os_libs/PDFManipulation_native.zip", which actually does not exist on system.
  
  
•  "log_bootstrap.0.log" shows that it hang at deletion.
  
  [Jul 24, 2025 10:02:50 AM] Starting to synchronize native files
  [Jul 24, 2025 10:04:00 AM]       Synchronization of file [/usr/sap/<SID>/J00/j2ee/os_libs/*_native.zip]  finished. Size: 313 KiB / 320611 bytes
  [Jul 24, 2025 10:04:00 AM]       Error while deleting native file [/usr/sap/<SID>/J00/j2ee/os_libs/PDFManipulation_native.zip]
  [Jul 24, 2025 10:20:39 AM] Thread [Watchdog for main] initiated a full thread dump on [Tue Jul 24 10:20:39 UTC 2025] due to: [Watchdog timeout]
  [Jul 24, 2025 10:20:39 AM] Exception occurred for component [internal/unkown] of type [unkown]
  com.sap.engine.bootstrap.SynchronizationException: No progress was recorded since [ Tue Jul 24 10:04:00 UTC 2025]. 
  
  
• Manually creation of dummy file or increase the watchdog timeout value does not help.  
  
  
• ADS system itself is working fine in landscape.

SAP NetWeaver Application Server Java

SAP Java startup failure, synchronization binaries, element.resynch, No progress was recorded since, error while deleting. , KBA , BC-JAS-COR , Enterprise Runtime, Core J2EE Framework , Problem