A glitch with chunks is really affecting performance, causing the server to close...

A few days ago, I noticed that when I was running some Repeating Command Blocks inside a dancehall I was building, the chunks in the area glitched out, and when I came back there, the Repeating Command Blocks, as well as the Redstone Hoppers, Droppers and Observers I had connected to them were all gone. This problem doesn't end here, because since the blocks disappeared with the glitch, my frame rate had dropped incredibly, causing serious lag, and giving me only 1 frame per second at the most in the general area of the dancehall (X=-1000, Y=77, Z=-1000). And if I sit around for too long inside the dancehall, I will get a message telling me that my server got closed. I have also been getting the occasional "Connection Refused" error as well.