Cannot apply patch. Error message saying configuration folders are missing

I already have a ticket open with Manage Engine, but I am not making much progress on resolving this issue. When trying to apply a patch with UpdateManager.bat, we get an error: "Patch cannot be applied as some dynamic configuration folders are missing.Contact support for further assistance."

When ManageEngine examined my logs as part of the ticket, they noticed there were many lines showing jar files being locked by a process. They thought maybe I didn't do enough to make sure all process and services were shutdown. Here is an example of the last sever lines of my updatemangerlog0.txt file:

Mar 5, 2021 10:15:19 PM [com.adventnet.servicedesk.updatemgr.util.SDPatchValidatorUtil] [WARNING] : File D:\Program Files\ManageEngine\ServiceDesk\lib\tomcat\ecj-4.6.3.jar is locked by [NativeFileManager.Process(pid=3240, name=Zulu Platform x64 Architecture)]

Mar 5, 2021 10:15:19 PM [com.adventnet.servicedesk.updatemgr.util.SDPatchValidatorUtil] [WARNING] : File D:\Program Files\ManageEngine\ServiceDesk\lib\yuicompressor-2.4.2.jar is locked by [NativeFileManager.Process(pid=3240, name=Zulu Platform x64 Architecture)]

Mar 5, 2021 10:15:19 PM [com.adventnet.servicedesk.updatemgr.util.SDPatchValidatorUtil] [WARNING] : File D:\Program Files\ManageEngine\ServiceDesk\lib\zsec-pml.jar is locked by [NativeFileManager.Process(pid=3240, name=Zulu Platform x64 Architecture)]

Mar 5, 2021 10:15:19 PM [com.adventnet.servicedesk.updatemgr.util.SDPatchValidatorUtil] [WARNING] : File D:\Program Files\ManageEngine\ServiceDesk\lib\zseclogger.jar is locked by [NativeFileManager.Process(pid=3240, name=Zulu Platform x64 Architecture)]

Mar 5, 2021 10:15:23 PM [com.adventnet.servicedesk.updatemgr.util.SDPatchValidatorUtil] [INFO] : Migration aborted due to dynamic configuration folders are missing. This may create issues during migration, so aborting now

Mar 5, 2021 10:15:23 PM [com.adventnet.persistence.DefaultPatchValidator] [SEVERE] : Patch cannot be applied as some dynamic configuration folders are missing.Contact support for further assistance.

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I have taken as many steps as I can think of to make sure the services are shut down, but this error persists. I'm getting close to a time limit here. I need to get this update in place. Any advice would be greatly appreciated!