Flower beds in the run/range are "enrichment". Solutions are :
net the flower beds (less attractive, more difficult to work them seasonally);
don't place flower beds in the range (my solution) or gardens, either;
try and plant things they won't dig up, or can't dig up, and won't eat, which are none the less attractive and suited to your planting zone (likely a very short list)
To do otherwise is to blame the dog for digging holes in the yard when you keep handing him the bones to bury.  A flower bed, to chickens, is an attractive nuisance.  Either they want to eat the leaves, the flowers, the bugs among the plants, enjoy the shade, or bathe in the dirt.  Gardens are good for all those things - can hardly expect the chicken to not be chickens.