Well, this can either mean that the chunks have been deleted/are corrupted or that is all just visual and there isn't anything to worry about.
so... first things first: backup your world. Also, give us a log when it happens those things may reveal something.
After those things are done you can try to force load them by placing a block inside them. Especially if you know where blocks are and try to place new blocks on them can show if its just visual or if something else is going on.
Also, try to open it world in mcedit. I'm pretty sure that this is a bit more forgiving when chunk files are damaged in some way and may even be able to restore them (I go from memory on that one and I don't know for sure if it has that ability and how well it works on vanilla let alone on modded if it has it. Make sure you have a backup)
If all else fails and no one finds something in the logs the last thing you can do is upload the world, maybe someone more knowledgeable is willing to take a look him/herself.