So, I have played around with RemoveFile. The current situation is that 
the old shortcuts are called SCINodeManager.bat and SCINodeManager.log. 
Adding 2 RemoveFile sentences inside the component fixes the issue:
          <Component Id="compshortcutsNodeManager" 
Guid="EC9C5D40-7558-4040-93C2-1D320E890C08" DiskId="1">
            <CreateFolder/>
            <RemoveFolder Id="dkw4" On="uninstall"/>
            <Registry KeyPath="yes" Id="ice38csNM"
                Action="write" Root="HKCU" Key="Software\Dolphin 
Interconnect\Installer\ice38csNM" Type="string" 
Value="[ProgramMenuFolder]"/>

            <Shortcut Id="shnodeman" Description="Restart dis_nodemgr 
service" Directory="SCIUtilMenuFolder" Name="SCI23" 
LongName="dis_nodemgr.bat" Target="[!_cutilbatch]" 
Arguments="dis_nodemgr" IconIndex="0" Advertise="no"/>
            <Shortcut Id="shnodelog" Description="Display dis_nodemgr 
log messages" Directory="SCIUtilMenuFolder" Name="SCI2231" 
LongName="dis_nodemgr.log" Target="[_DISnotepad]" 
Arguments="%SystemRoot%\system32\drivers\etc\DIS\log\dis_nodemgr.log" 
IconIndex="0" Advertise="no"/>
            <RemoveFile 
Id="compShortcutsNodeManagerSCIUtilMenuFolderRem1" 
Directory="SCIUtilMenuFolder" On="install" 
LongName="SCINodeManager.bat*" Name="SCI23"/>
            <RemoveFile 
Id="compShortcutsNodeManagerSCIUtilMenuFolderRem2" 
Directory="SCIUtilMenuFolder" On="install" 
LongName="SCINodeManager.log*" Name="SCI2231"/>
          </Component>

But note this:
  if the LongName does not end with a star symbol, then the shortcuts 
are not removed. I compile with WiX 2.0.4820.0.

Calin Iaru wrote:
> I recently had to rename the some applications and the corresponding 
> shortcuts. The problem is that after an upgrade, the renamed 
> applications are installed, the old applications are deleted, but the 
> old and new shortcuts coexist. You will find below the component definition:
>
>           <Component Id="compshortcutsNodeManager" 
> Guid="EC9C5D40-7558-4040-93C2-1D320E890C08" DiskId="1">
>             <CreateFolder/>
>             <RemoveFolder Id="dkw4" On="uninstall"/>
>             <Registry KeyPath="yes" Id="ice38csNM"
>                 Action="write" Root="HKCU" Key="Software\Dolphin 
> Interconnect\Installer\ice38csNM" Type="string" 
> Value="[ProgramMenuFolder]"/>
>
>             <Shortcut Id="shnodeman" Description="Restart dis_nodemgr 
> service" Directory="SCIUtilMenuFolder" Name="SCI23" 
> LongName="dis_nodemgr.bat" Target="[!_cutilbatch]" 
> Arguments="dis_nodemgr" IconIndex="0" Advertise="no"/>
>             <Shortcut Id="shnodelog" Description="Display dis_nodemgr 
> log messages" Directory="SCIUtilMenuFolder" Name="SCI2231" 
> LongName="dis_nodemgr.log" Target="[_DISnotepad]" 
> Arguments="%SystemRoot%\system32\drivers\etc\DIS\log\dis_nodemgr.log" 
> IconIndex="0" Advertise="no"/>
>             <RemoveFile 
> Id="compShortcutsNodeManagerSCIUtilMenuFolderRem" 
> Directory="SCIUtilMenuFolder" On="uninstall"/>
>           </Component>
>
> I would greatly appreciate your assistance.
>
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