That's good that she has no cage mates. and Yes, Definitely do keep her lay box in the cage for the meantime. What substrate are you using for her and her lay box? What type of
UVB bulb do you have? Coil or tube? T8 or T5? How old is it? Is your vet a reptile vet or a "exotics" vet? or just a regular dog or cat vet?
From what I have read, Females can reabsorb the eggs if they are not given a suitable area to lay them. Usually they will just lay them wherever, but some might hold on to them and get eggbound, and some might absorb the eggs over time. If Your dragon is egg bound you MUST get those eggs removed. If the Follicles turn into eggs and do not drop into the oviducts they could rot inside her belly and kill her. The Most common symptoms of egg binding is not eating, Lethargy, Unresponsiveness, or Appearing stressed out.
I'm no expert on Dystocia (egg binding) you should probably PM someone who knows more about this than me such as EllenD, Drache613, AHBD, Kingofnobbys, or Cooperdragon, I Bet they will know what's going on as they have had YEARS of experience and have a TON of knowledge about bearded dragons.
But mainly just keep giving her calcium and multivitamin+UVB and hopefully she will be back to normal.
-HippieLizards.