Reset NTFS permissions to factory default on entire system partition?

I'm having occasional problems with NTFS permissions on a Windows 10 PC, especially when installing programs.

I guess it started when I created a new user for myself some time ago and deleted my old user, after a certain program failed to install, also because of a permissions problem.

Since then, I have occasionally tried and manually changed permissions here and there in case of access problems. In the meantime I have learned that one should not do this (unless you know exactly what you are doing).

Now I'm looking for a way to reset all permissions on the entire system partition to factory defaults.

As I have learned, this seems to be possible with the command

Secedit /configure /db Secedit.sdb /cfg C:\windows\inf\defltwk.inf /overwrite

However, before I unleash that command onto my system drive: could doing this possibly also go terribly wrong, or should I expect any severe side effects, respectively?

You should expect severe side effects from any global manipulation of permissions on the system disk.

As precaution, I suggest to take an image backup of the entire system disk using a product such as AOMEI Backupper Freeware, make its bootable media, and test booting it to see that it can see both the hard disk and the backup image, just in case you will want to restore the last working version of Windows.

From studying the contents of defltwk.inf I got the impression that it only resets some permissions, but not everything.

I suggest using the third-party product Tweaking.com - Windows Repair Free/Pro, free for personal use.

If everything fails, Do a Repair Install of Windows 10 with an In-place Upgrade. This is exactly the same process as doing a major upgrade of the Windows version, even if it will upgrade the current version to itself.