Yep, I'm afraid I haven't been able to find a way. To have a consistent state, you can manually install all the updates by cross-checking the images (a boooring task to do) or you can use dism/powershell to extract the installed package from the wim image, then take that output and use Get-CMSoftwareUpdate and Set-CMOperatingSystemImageUpdateSchedule to schedule the updates ( Note: the latter cmdlet is available only for SCCM 2012 R2). SCCM will first perform a detection whether the update is already installed, and will skip it if it is already applied. After this, the updates will show as installed, but with no install date. Also, the available updates counter for the "Schedule Updates" option will be adjusted. Still better than nothing.
Thanks for the info anyways