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I had failing hard drive and managed to extract the data from it using Linux. I have tried Macrium Reflect which wasn't successful, as the clone failed. So, in Linux I finally managed to get the contents from the old drive on the new one. The system boots fine with the new drive. However, the permissions on the folders are different than before.
How I can reset them?
P.S. the old failing drive is still somewhat operational, I can get data from it as external drive but can't boot from it (the machine loops on POST, drive clicks, won't load at all). I managed to get image of it as is, and can access its System Restore points. Unfortunately, it seems that System Restore works per drive.
Thank you!