I had this strange issue on Windows 8/10 where changes such as file/folder renaming or deletion not appearing after a modification. A manual “Refresh” from the contextual menu (right click + Refresh) was required to show the last modification.
It seem that some Windows core components were corrupted and needed to be repaired/restored.
First of all, I would suggest to look at the Event Viewer (under Control Panel > Administrative Tools) to see if any disk or NTFS related errors show up. If you have a unhealthy disk about to die, cloning the disk and replacing would be the first step to do prior doing the procedure.
To resolve this matter, open the Command Prompt with elevated privileges and do the following, one after the other upon completion of each commands :
dism.exe /online /Cleanup-Image /StartComponentCleanup
dism.exe /Online /Cleanup-Image /RestoreHealth
Reboot your computer once completed, this should have resolved the issue.