Invisible blocks / Can fall through terrain

[Es-Ypsilon]

It seems when my world generated, there were several areas where no block texture was created. Also, these blocks do not have any collision detection, but I can "pick up" invisible dirt blocks with a shovel. This only applies to the sides however, as the top layer of blocks have texture and collision detection, can be picked up with a shovel but... they do not disappear, meaning the texture is still there and can be walked on, yet cannot be picked up with a shovel twice.
Follow me on my journey to the transparent center of my earth:

http://steamcommunity.com/sharedfiles/filedetails/?id=1313349238

http://steamcommunity.com/sharedfiles/filedetails/?id=1313350050

http://steamcommunity.com/sharedfiles/filedetails/?id=1313350312

http://steamcommunity.com/sharedfiles/filedetails/?id=1313350665

There is another area on the map (which I couldn't find at the moment) with a way larger proportion of those bugged blocks, you can actually see through the whole mountain there.
Is there any way I can recover my world or am I stuck with unminable, invisible fall-through blocks?