We don't know of anything that can cause villagers to mysteriously be wiped out. If you were playing constantly, your villagers had plenty of food, and you had a healer to heal any sick villagers, they should have been fine.
The most common causes of villages being wiped out are:
1. Having only one trained farmer. If the farmer gets sick and is not healed, starvation is a real possibility for the tribe. Villagers can (and should) be trained in more than one skill. In VV3, any villager with farming knowledge will harvest food when the food supply is critically low.
2. Not having a trained healer to take care of the sick when the game is off. If you're using kids to heal sick villagers when the game is on, you need to be aware that kids will not heal sick villagers on their own. If there isn't a trained adult healer, you need to be vigilant and check frequently for sick villagers. Keeping the fire going reduces the frequency of disease.
3. Growing the population too large and too soon. The initial food supplies in all VV games are limited and won't support a very large population. In VV3, if you grow the population beyond about 10-12 villagers, you will need to hunt mushrooms a lot to prevent starvation.
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Barbara
Unicorn
Last Day of Work