How to best manage folder and file security

I constantly struggle with deleting folders or files due to permissions.  For example I was testing our backup software and restored a backup of one folder with multiple sub-folders.   I tried to delete the restored folders and every folder except 1 deleted.  Inside the folder that didn't delete were sub-folders.  
I checked the security on the root folder and domain admins and everyone had full permissions.   I checked the box "replace all child object permissions".  When I clicked apply, I got the message "failed to enumerate objects in the container Access denied".  I checked and 3 of the sub-folders that had more sub-folders in them all had the permissions from the root folder.   The last sub-folder displayed "you must have Read permissions to view properties of this object"

This is not uncommon.  So my question is how do I change permissions all the way from the root to all sub-folders without having to do them one at a time?   Is this  Windows issue?