There is a way to fix this, but usually not from within Ubuntu.
Files being removed aren't actually removed. They are just marked as removed and the space they took up on disk is being marked as "free". So as long as you don't write in that space, the file is physically still there, but the disk (and therefore the OS) doesn't know about the file.
You can use NTFS recovery software to restore many of the files lost. There're tools running on Ubuntu or Windows. There're tools for free and those you have to pay for. They differ greatly in how much data they're able to restore and how long it'll take. Usually Windows-native tools work better, since NTFS is an invention by Microsoft and there's no 100% native support for it on other operating systems.
I've had great success with a software called GetDataBack NTFS 1 (now called GetDataBack Pro Data Recovery it seems, I'm not affiliated). It took about a day to search a whole 1 TB drive for files and about another day to actually recover those files to a 2nd drive. About 85 to 95 % of the data deemed to be lost was recovered. Other tools I'd tried only managed to recover up to 30 to 40 % of the data.
How to recover
Try to prevent any write access to the affected drive to avoid the "deleted" files being overwritten. There're ways to mount a drive in read-only mode (how to do this on Windows or Ubuntu), but it can be sufficient to not write on the disk intentionally in this case.
- Turn off the machine with the affected drive
- Remove the affected drive from your machine and hook it up in another machine.2 Make sure that machine won't boot from the affected drive.3
- Start up the other machine
- (Optional: Mount the device in read-only mode as mentioned above)
- Run the recovery tool of your choice to analyze the affected drive
- Restore the files found to just another (3rd) drive (doesn't matter whether internal or external)
- Copy any required files from the 3rd drive back to the affected drive at the correct place
This assumes you want to continue using your affected drive as-is. Actually you should skip step 7, use the recovery tool to restore only the most important files and then proceed to fully erase the affected drive and install a fresh copy of Windows, then proceed to copy the restored data back (make sure to make a backup of the non-deleted files you'll need).
Note: There are other tools being able to find and restore deleted files from within Ubuntu (either your local installation or a live usb/disc), which are free to use. When I tried them, they either took exceptionally long to find files at all or found only a small fraction of what was lost. YMMV
1 The software costs about USD 80 for a lifetime license, which is absolutely worth it imho. You only need to purchase it to actually restore the files, though. You can analyze your drive for free and get a file tree you can search through to check if the files you need to recover have been found. Again: not affiliated, just a happy user.
2 The operating system required on the 2nd machine depends on the recovery software being used, e.g. GetDataBack runs on Windows.
3 You can usually open a boot menu to select your booting drive at startup of the machine via pressing a certain button on your keyboard. Usually this is
F12 nowadays, but the exact key may differ for your specific main board. Consult the manual to find out which key to press. You can also set up a permanent boot order (setting the order of devices to check for bootable operating systems) via the BIOS/UEFI settings of your main board, also accessible via pressing another specific key during startup (usually
DEL). That key also differs, though, so make sure to check your main board manual.