This article goes over how to properly prepare a client for imaging, which if you're making full clones in a VDI. http://technet.microsoft..../library/bb694095.aspx
However, you asked specifically about linked clones, which can be prepared using quickprep, which basically just changes the SID and creates the new computer account in the domain. As you've noticed, this process doesn't change the SCCM client GUID, which results in duplicates in the SCCM console. If you're using linked clones that aren't assigned to any user, I'd think about whether or not to even have the SCCM client in the base image. It probably wouldn't be worth it because, any time you want to make a change to a pool of non-persistent desktops, you'd just change the parent image and recreate the pool. Also, the pools can change so frequently, it wouldn't be much help from an inventory standpoint.
Now if you're using linked clones with persistent users, this exactly describes the situation you'd be looking at. I'd suggest a running a script that you can run to strip out the unique SCCM GUID as a part of the quickprep/sysprep process. Here's a batch file I use which relies on ccmdelcert.exe, which I believe can be found in the SMS toolkit.
rem Clean unique SCCM client data
net stop Wuser32
net stop CcmExec
del %windir%\smscfg.ini /f /q
del %windir%\system32\ccm\logs\*.* /f /q
Alternatively, here is a VBscript that I haven't tested which fixes remote machine duplicate IDs without the use of ccmdelcert.exe. http://www.blogmynog.com/...plicate-smssccm-guids/
In SCCM 2012 there are some improvements that will automatically identify which clients are virtual, but I'm not sure what impact that would have on the GUID generation/duplicate issue you've raised. I'll see what I can find on that.
<message edited by elgwhoppo on Monday, October 15, 2012 12:16 PM>