Terrible implementation of what you call "backup".
In all other areas of IT, "backup" means making a copy, and leaving the original file intact. MS chooses to (1) move files to different locations (2) without informing the user, and (3) without giving him/her the choice during initialization how to do the backup.
For each file in the specified directories, make an online backup while leaving the original file 100% untouched. Keep track of changed files since previous backup, and sync changes with regular intervals (configurable, default daily).