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    Cloning a drive should have been straight-forward if you had physically replaced the disk. As it is, I suggest to Do a Repair Install of Windows 10 with an In-place Upgrade.
    – harrymc
    Commented Sep 29, 2020 at 16:50
  • @harrymc Windows 10 by itself is fine, the cloned drive was a completely different partition than the system disk. It's just the UWP apps on it that are "missing". Commented Sep 29, 2020 at 16:59
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    Repair install will restore the registry. I hope you haven't left the old disk in its place.
    – harrymc
    Commented Sep 29, 2020 at 17:01
  • Wouldn't a system restore just keep the current paths? As far as Windows is concerned the apps are just "offline" and stored on the old drive, it has no reason to look after them on a completely different disk. Commented Sep 29, 2020 at 17:06
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    If the old disk is disconnected, and the new one is connected in its place, this should set Windows to a consistent state.
    – harrymc
    Commented Sep 29, 2020 at 17:11