Step1, From SCCM, create a new script under software library.
Here is a script body.
reg delete HKEY_CLASSES_ROOT\ms-msdt /f
Step 2, use CMpivot to create a new collection.
Now select a computer collection, perhaps start with a small collection, right click and start CMPivot.
On query window type script below and run.
Registry('HKLM:\SOFTWARE\Classes\ms-msdt') | where Property == 'EditFlags'
You might ask why we are checking KHLM not HKCR. Here is a reason:
HKEY_CLASSES_ROOT is not a real physical hive (it stores no data), it is just a merged view of
HKEY_LOCAL_MACHINE\Software\Classes. Updates to the underlying keys are instantly visible in
HKEY_CLASSES_ROOT. (source: https://stackoverflow.com/questions/50146334/how-to-update-hkey-classes-root-after-a-new-subky-is-added-to-hkey-local-machine)
In fact, you can't query HKCR using CMpivot, it will return nothing.
Once you got list of systems, on the top right corner of the CMPivot, click "Create collection"
Give it a good name and create the collection.
Right click the collection you created and run the script you created from the Step 1.
Keep doing this against all systems.