I've decided to keep the old ipad so I won't be trading it in. Can to $90 value given me be deducted via my Apple Card?

You're not addressing Apple here. This is a user to user tech support forum and we, just users like you, are not aware of your agreements/transactions with Apple trade-in.

Please contact Apple support directly and explain your problem. Use this link:--> Get Support

Thanks and regards

Giulio