2047880 - The upgrade stops due to sap.com/ui~five application issues when upgrading

The upgrade of NW AS JAVA fails and the error below has been logged to the SUM traces:  

Cannot deploy two applications with identical application aliases (context roots). Your application [sap.com/ui~five] defines an application alias (context root) [sapui5] that is already in use by application [JavaEE/sapui5]. There are two possibilities in order
to proceed with deployment: 1) Define different application alias (context root) for your application [sap.com/ui~five] (this is the preferred option). 2) Undeploy the application [JavaEE/sapui5]. Create an OSS message in component: BC-WD-HTM for support.

Or in a thread dump you see thread below always in RUNNABLE state:

"DeployThread[sap.com_ui?five]"
user="Administrator" isapplicationthread="true"
java.lang.Thread.State: RUNNABLE
at java.io.WinNTFileSystem.delete0()
at java.io.WinNTFileSystem.delete()
at java.io.File.delete()
at com.sap.engine.lib.io.FileUtils.deleteDirectoryAndReturnRemainingFiles()

SAP NetWeaver Application Server Java

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