Since Windows is presenting these errors I'd look to get my SQL Files off that drive and then run CHECKDB against all the databases that were there. I'd also do test restores of the most recent backups of those databases and run CHECKDB against them to make sure my latest backups are of good databases.
The possible reason for NTFS error is corruption hence you need to repair Windows OS and after this you can restore it from updated backup. If you don't have a backup then you must go with external tool.
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