I had a Secure Boot problem and followed troubleshooting steps that involved running commands in Command Prompt: `mountvol S: /S`, `del S:*.* /f /s /q`, and `bcdboot %systemroot% /s S:`. The deletion appeared to be removing many files, so I restarted the computer before the process was finished. Windows then reported that no operating system could be found. I was eventually able to repair the Windows installation using a bootable drive, and my personal files are still present. However, most installed applications no longer work, and their shortcuts report that the target cannot be found. Is there a way to restore the applications, or do I need to reinstall Windows and all of the affected programs?
2 Answers
Those commands likely deleted files from the EFI system partition, and possibly more depending on how the drive letters and wildcards were interpreted. Repairing the Windows boot files can make Windows start again, but it does not restore deleted application files, registry entries, or shortcuts. Back up your personal data immediately, check whether the program folders still contain their executable files, and then reinstall any damaged applications. If important files were deleted, stop writing to the drive and consider professional data recovery or file-recovery software before doing a clean installation.
If an application’s installation folder and executable are still present, you may be able to launch it directly and recreate the shortcut. Many programs, however, depend on registry entries and shared components, so reinstalling them is usually the reliable fix. Do not delete the existing folders until you have copied your personal data and checked whether the installer can repair the program.

I was able to repair Windows, but the applications and shortcuts still report that their targets no longer exist. The commands came from Microsoft documentation, although I may have interrupted them or entered them incorrectly.