If the frames have seperated, top from side pieces I'm guessing, the comb should be still attached to the foundation and the wood parts, are they not ?
Saying that the" bees built comb all over "? are you saying that the bees joined the frames together comb to comb or what ? They will do that even if the frames are intact.
If the frames are joined together top and bottom, with comb, top box and bottom box, you will tear some of it apart when you lift the top box off. Have you lifted the top box off to make the swap already? If so maybe it would be better to let things go as they are for the time being. The bees really don't care because they will provide space for themselves if needed. They will also continue to store honey if there is a flow going on and there seems to be according to your explaination of hive activity. Bees don't build comb if there is no need.
It depends on the temperature in your area for guidance on how long you can keep the boxes open. I'm thinking that the temp. must be at least above 50 degrees if there is all that hive activity as you describe ??? You should give some indication of the temperature for advice in that vein.
In the future, after the honey flow is over, you could pull out the damaged frames one or two at a time and replace them as long as there is no brood. If there is some capped honey in the comb without brood and pollen that could be extracted or stripped off the foundation if the frames are too badly damaged to hold together in the extractor. Or you could feed the honey back to the bees by placing the inner cover above the brood boxes, placing another box on top of that and put the damaged frames in that. The bees will climb up and clean out those frames and move the honey back down through the inner cover hole. That would prevent robbing if that is a concern.
About the best I can do while guessing. Good luck.