Villagers disappeared
Solution 1:
There are a few stories I have heard like this, there are a few possibilities: 1) Zombies have attacked your villagers. 2) The villagers despawned Ahh, villagers aren't supposed to despawn, but I have heard stories, one story heard says that this occurs when you download mods, as a glitch. Also it might occur if you have a mod that is SUPPOSED to make villagers disappear! Since you have mods, the mod being the fault is likely, but not 100% so. For example, If you switch between game modes or difficulties, there is a glitch that causes villagers to despawn. Hope this was helpful!
Solution 2:
I looked, and I don't believe that any of your mods have deliberate options to de-spawn villagers. This is what I recommend you do; basically all you can do when you hit weird glitches that are probably caused by a mod, or a combination of mods being loaded:
- Create a new, vanilla world with no mods loaded
- Go somewhere you can easily reproduce the weirdness and set your spawn point there (or use a command to set the spawn point for the world). In your case, go into creative and fly around until you find two villages you can
/tpbetween to test. - One by one, load the mods, wait for the weirdness to happen (in this case, villagers de-spawning)
- You (in theory) identify the culprit
You probably want to remove any chunk loaders, if you have them running. Actually, I'd start with that and see if it clears up.
It's a bit of a long process, especially when you have 20+ mods installed. Going through your list, I'm pretty certain the following aren't the culprit:
- Bibliocraft
- BuildCraft
- ComputerCraft
- Damage Indicators
- Forge
- Natura
- Optifine
- Portal-gun
- The Twilight Forest
- What Am I looking At
- Applied Energistics
- Fungeon Pack
- Nether ores
- Smooth Bedrock
- Hats
- Gravity Gun
- Armor Status HUD
I play these mods pretty regularly and while some are known for glitch and lag, I've never seen them interfere with the actual game.
Hate not being able to zoom in on one in particular, but I can't find mention of any of them having this specific problem (in fact the only result for several searches leads back to this question).