Note to self:
When you choose to redirect the Application Data folder the certificate store folders are NOT redirected. They will reside in the default folder.
Personal Certificates are stored under following locations:
%userprofile%\AppData\Roaming\Microsoft\SystemCertificates
%userprofile%\AppData\Roaming\Microsoft\Protect
%userprofile%\AppData\Roaming\Microsoft\Credentials
%userprofile%\AppData\Roaming\Microsoft\Crypto
%userprofile%\AppData\Roaming\Microsoft\CLR Security Config
%userprofile%\AppData\Roaming\Microsoft\CryptNetUrlCache
HKEY_CURRENT_USER\Software\Microsoft\Cryptography
HKEY_CURRENT_USER\Software\Microsoft\Protected Storage System Provider
HKEY_CURRENT_USER\Software\Microsoft\SystemCertificates