This problem can happen if the number of characters in the complete file path exceeds 260 characters.
Moving files from Linux to Windows can cause the limit to be byassed, until you try to open it.
The delay in opening "good" folders and files is interesting...it should be almost instantaneous.
It could also be a result of some kind of physical damage to the drive.
One thing you could try is to create a new parent directory, and 2 sub directories in another location on the drive
Make the folder names short.
If you can copy files to those two locations, it may indicate the 260 character boundry is the issue.
If so, there is a registry fix...
Open regedit and navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem
Hightlight the location and right-click. Select Export.
Give it a simple file name and select your Desktop as the location.
This is your backup.
Look for a key called LongPathsEnabled and set its value to 1 (one).
If it's not there, right-click on FileSystem, select New, then DWORD
Name it LongPathsEnabled and set its value to 1.
Reboot.
