Mcedit Help

Okay, I recently downloaded mcedit and were playing around with it for a little but eventually gave up on trying to figure it out myself. When I was playing minecraft the other day, I saw what I thought was one of those light bugs so I went to go break a block in the chunk but nothing happend. Then I realized it was different. It was a big perfect square that went down really far and there was blue like the sky at the bottom. When I went over to the square everything was dark and It was kind of like being in the void. I figured I must have done something with mc-edit but I didn't remember being in the area that the big hole-square was when I was playing around with it. I can place anything in the square but I can break blocks around it. When i'm flying and I fall I start falling really slowly. I also cant go down once a reach a certain point. and now there are like tons of bats flying in it. PLEASE HELP ME! This is ugly looking and it consumed half of my house.Thx EDIT: So In mcedit I covered the part up with grass and it looked fine. While playing minecraft it still shows the black, empty chunk. Then I realized something. Whatever I placed in the black chunk on mcedit. It appeared on another chunk a little bit a way while playing minecraft. When I do mcedit the empty chunk and they placed parts in the other chunk are shown but when playing minecraft only the displaced blocks are visable. Also, while doing mcedit I can go near the bottom of the chunk and it shows the terrain and blocks from the chunk where the stuff I put in the empty chunk are.