If the removal of the Trusted Application configurations is required it is possible to do so by executing the following two lines in a powershell instance on the Front End:
Get-CsTrustedApplicationPool | Where-Object {$_.Applications -like "*SkypeShield*"} | Remove-CsTrustedApplicationPool -forceGet-CsTrustedApplicationPool | Where-Object {$_.Applications -like "*sipfiltertrustedapp*"} | Remove-CsTrustedApplicationPool -forceEnable-CSTopology