Add or Remove Search Index Locations in Windows 10  

Steve C said:

Indexing misses some of my user folders despite then being selected for indexing, I've rebuilt the index to no avail and run the troubleshooter. Any ideas?

Hello Steve,

Odd. Seems like there may be some sort of access issue.

Did you move these folders to another location that the default, or have them protected (backed up) by OneDrive?

Steve C said:

The offending folders are under My Documents on my D: drive along with other folders which are indexed. I don't use Onedrive for backup. The files are found in the search box for Classic Shell but not in the Cortana search box.

Odd. Did you select the Documents folders and others from the D drive location?

Normally, this below is checked by default, but it would hurt to check if is for the D drive.

Steve C said:

That box for D: isn't checked. Should it be since I thought that enabled indexing of contents?

It was just something to see as a test for how it behaves after being checked.

Steve C said:

That user directory did not have permissions for System or Administrators. What are the default permissions for a user directory other than the account user and is there a simple method to reset them to the defaults?

You could try the context menu added below to restore the default permissions of the folder.

Add Reset Permissions to Context Menu in Windows