Nick Papatonis:
To do a full before/after comparison, you also need to look at the permissions. It's usually the permissions on the ProtectedRoots (PR) key that get cleaned up. I watch screenshots of the registry Perms>Advanced displays.
The PR:Certificates value is a binary encoded list of the user certificates in Root/Certificates. My notes from observed values:
=Summ; ProtectedRoots.Certificates usage
#CryptSvc PR.certs
PR has (only) a "Certificates" data item
PR.cert first 24B always 18 00 00 00 * 18 00 00 00, len=24B+20B*cert#
cert20B= cert.key= cert (.cer sha1) thumbprint
The binary Certificates begins with 24B, which begins and ends with
18 00 00 00,
For each certificate, append the 20B sha1 thrumbprint.
Most users don't have any personal certificate authority certs. These will be under the Root/Certificates, before you do the Root delete cleanup.
If you used the powershell script to do the repair, it saves and restores Root/Certificates, and the PR:Certificates binary list is rebuild accordingly.
The script also dumps/save the old permissions to ProtRoots.log. If you rerun the script, it will append the new values (before the repair) and you can look in the log for the before/after snapshots.
If you want help with the script or log, tag in on the Chrome CryptSvc help thread here.