HigginsHere

In regards to this problem, it has been confirmed that it has to do with a SecretRooms mod conflict. Disable the mod to remedy the problem, and make regular backups as a fail-safe.

This sounds familiar, though this is just a shot in the dark: Have you been messing around with rifts at all?

Like David said, I really don't think it has anything to do with dungeons, or even battletowers for that matter. Through some of my own tests, (on a LAN server) my brother and I kept messing around in other dimensions, logging in and logging out, then exiting the dimensions to either crash or lag. After said crash or lag there would always be a fresh chunk (sometimes with a battletower) right smack in the middle of our base, much to our chagrin. But after disabling SecretRooms, the error/crash completely stopped. We've been playing for hours since with little to no problems. I wish I knew how far spread this problem was, but considering the scarcity of bugs, it seems fairly large. Edit: I would be remiss if I didn't mention that we did have at least two blocks from SecretRooms in the chunk that would get reset/overwritten.

Hey, I really doubt this is the solution to all, but it seemingly has been the solution for me. My brother and I were able to replicate the chunk reset to the T by using a portal log-in/log-out system. Through the basic process of elimination, we found out that when the mod "SecretRooms" was disabled, the chunk reset/error/whatever stopped doing its dreaded griefing. We're still on the look out and are very hesitant to let our guard down, so there will be continuous backups. But in the mean time, it seems as if we've solved our problem. I really hope this helps someone else.