I know that MFD need to communicate with their server to authenticate the license, ...
Not true. Once Manifold is activated, it doesn't care if you never go online again. (And indeed you can activate without ever going online, if you choose. But I digress.) What you have is a broken Windows installation that you've partly recovered. It's not the same after recovery (it might take a week to work out why, but it might well be hard-disk related), and Manifold doesn't recognize the system. There's nothing you can do to fix that now. You'll need a new Windows installation (probably) then a new activation of Manifold (definitely). And then... how about using imaging software, so that if and when this happens again, you can recover everything (including activations) in 20 minutes? I'd recommend Terabyte Image for Windows. P.s. check your hard disks thoroughly before the new installation. One of them might be failing, or about to fail (that's a guess). Check the SMART attributes for each drive, especially the CRC errors (should be 0).
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