Be careful, your ammunition factories and oil derricks also have their own storage capacity, if you do not recover their productions they are lost during raids because they are not protected. 

viradium77 said:

Badlands, Plarium.com

Bunker is built up to protect 35000 resources

I get raided with less than that amount on base and I still lose resources.

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Hello, Commander!

If you raid a Base where all resources are protected in a Bunker, you get a resource bonus for your raid. These resources are not deducted from the raided Base.