How to clone a minecraft world with new chunk files?

I have this problem with my world on minecraft where i walk to a certain place and then i just start lagging. It normally does not do this, but since i built a house there, it started lagging. I tried deleting the chunks in MCEdit and then entering minecraft again to rebuild it, and then importing a schematic of the house, just so it's back to normal but with new chunks. It still lags. The mystery here is that the place never lagged before, i used to get 80-100 fps now i'm getting the same but with super frequent jumps to 0 fps that last from a split second to 10 seconds. It's almost unplayable. I tried other solutions but none worked. So i guess maybe something's wrong with my save?

That's why i'm asking if there's any tool out there that can scan my save to rebuild it but with new files? I don't want to lose the save, and i don't want to box off the area because it's such a good spot!

Also, i never lag, even with 200-300+ entities, nothing. Can someone help me?

Make a seed for that world.