I just had a chunk reset also. At first I thought it was due to an out of date mod, but I upgraded all last weekend and it happened again.
Currently have loaded
MC1.6.4
Forge 9.11.1.965,
AE r14.finale3,
IChunUtil 2.2.0,
IC2 2.0.370,
TC4-4.05b,
Forestry 2.3.1.0-698
Highlands 2.1.4,
ChickenChunks 1.3.3.3,
PortalGun2.0.1,
EnderStorage 1.4.3.5
GravityGun 2.0.0
Natura 2.1.14
and a lot of other things that probably aren't the cause.
The chunk that was reset had a lot of Silverwood Nodes (still in the wood) I had grabbed with gravity gun. This chunk had reset before and had been painstakingly rebuilt. Sigh!
However, the problem happened previously (before the upgrades) in a different chunk that only had a Nether Portal and a bunch of oreberry bushes, otherwise vanilla.
The biggest problem is there isn't any sign of a fault since the game is saved OK but restored with a reset chunk. I don't know where to look to see what was going on when the error happened.
Any ideas what might be happening or, better yet, how to get feedback to the mod author?
MM