Cryptic has said countless times in the fourms that a discharged ship obtained via the VA token would not be redeamable. This was also the rule before F2P. If I discharged a ship that I bought with energy credits I would have to pay the same number of energy creds to get it back. Same thing here. You discharge a Tier 5.5 ship you bougth with a token you either A. Have to buy the ship which costs x C-points, or B spend a token. However you already used your token, so the only option is to pay the C-ponts.
Just like a Tier 4 ship, it costs X dilithium, but you got it with a token, if you want it again it is X dilithium.