I was using Botania R1.5-172, and everything was peachy, excluding for a bit of lag (Hadn't done any config work).
I updated to R1.6-174 and when I loaded the game up, I got the "These items are missing from this save"
When I started the game up, EVERY Botania item I had, had been removed from the world.
I do have Optifine, but I am sure that it cannot remove item IDs and such. It's Vanilla forge.
I have a few screen shots as well as the latest log.

FML Latest Log: http://pastebin.com/y56Sz5Kp

The empty spaces contained water and hydroangeas.

Corrupted file, download again

Okay, I used the in-game update prompt to update. I guess the crash a few minutes after corrupted it. If it's not one mod, it's another. I've been repairing my game after every mod update I do.

I really need to implement checksum verification sometime. Sorry for that.

Quite alright. Some things fall through the cracks. I just was like.. wut. I just couldnt tell if it was a corrupt file from the crash or the .jar was messed up and some other mod was overwriting it.

I've been wanting to make my own mod, but I have very little coding experience and am like a deer in headlights with some code. Plus I only have a few half baked ideas that don't amount to much