Reasons why dogs dig:
To stay cool or warm
It feels good!
First, accept that digging is a natural dog behavior. Your dog isn't doing it to punish you. Your dog is BORED.
3X more exercise than your dog gets now. Being in the backyard is NOT exercise.
Fence off your flower beds. Fresh turned dirt is Kryptonite to your dog.
If your dog must stay in the yard for hours, give her a BIG, GNARLY, GRISTLY, FROZEN FEMUR BONE to chew on. Think busy toys!!!! One empty Kong won't cut it.
Fill Holes with Lava Rock and feces. The rock is sharp and unpleasant to put paws on.
Give your dog her own Digging Pit. A 6'x3"X2' deep pit filled with sand is a great busy area for a "diggy dog". "Plant" toys, rawhides and filled Kongs in the pit to get your dog interested in digging there.