Do I have this right...you have a hen that is sitting on 2 sets of eggs? Going back and forth between 2 nests? (Silly girl).
You have several options:
1. Choose one clutch and toss the other.
2. Combine the clutches. (But you state that would be a very large clutch, so probably not the best option).
3. Candle all the eggs and set under the hen only those that are developed and look about the same in stage. You can then decide if you want to incubate the eggs that have some development but are not as advanced. (Best option in my opinion).
Toss any egg that is not developed.
My thoughts.
LofMc