The Windows Refresh feature really isn't worth the time it takes to do it. All it does is refresh the Windows modules, it doesn't reinstall any third-party drivers. Since third-party drivers are where 90% of Windows problems lie this make Windows Refresh useless as a way to recover a flaky system. Cloud Refresh is equally useless for the same reason. The only advantage of a Windows Refresh is that it doesn't affect your installed third-party apps - which is why people try it of course.
I what you accidentally removed in the Windows folder was third-party driver or third-party app related then Windows Refresh won't help at all. In your position I would make bootable installation media via the Windows Media Creation Tool, boot that media, delete existing UEFI partitions, and clean install Windows into the unallocated space that results. You will of course have to run Windows Update repeatedly, and across reboots, until no more updates are found. Then check in Device Manager that no devices have a yellow triangle with a black exclamation mark next to them. If any do, click the 'View optional updates' link on the Windows Update page, expand the Driver Updates section and see whether there are any suitable drivers in there.
Then of course you will have to reinstall all your third-party apps and copy back any user data you backed up.