Do you think these bills actually got deducted from their accounts?

Money is stored in computers these days, not bank notes. If the bank had $4,756,873,467,129 before the rats ate the bills out of the machine, the bank still has $4,756,873,467,129 after the rats eat the bills.

The money gets deducted from the bank when a person makes a withdrawal, not when they refill the ATM.

A bank note just means "the bank owes me this much and will therefore honor this as legal tender." It's meaningless before the bank actually issues it.