When my large base ship gets 3 Ion Tokens from an ion Bomb detonating, can it use SDV to discharge 1 Ion (so it only receives 2) and

avoid being ionised?

yes. just remember ion tokens are not round tokens, so they are not removed during the end phase. that means the ship would carry the two ion tokens until they are removed by some other means, or until it receives enough ion tokens to become ionized and perform an ion maneuver.

wow !!! thats huge !! i got Falcon and Uwing ionised from Ion Bombs by 2 Firesprays yday and got really p....ed !!!!