Local Personal Certificate Store: wiped after cutover

We are starting our migration with Pro Services and found today that after the cutover process, the Personal Certificate store had been wiped of certificates, which included the certificate issued to auth against our mail solution.  This is a massive issue for our remote workforce as these certificates take a long time to get and install from the provider.  This puts a hard stop on our migration as you could imagine.  How do we retain the cert store while using the tool?