Charge is getting created against the GIFT CARD authorization which was already reversed earlier

Answer

Example Scenario:

1. Order is placed with 3 Lines using the multiple Payment type, Gift Card (GC) + Credit Card (CC).
   
   
   
2. Order was created for the Authorization Amount: 306.57$ (GC: $200 CC: $106.57).
   
   
   
3. Order line canceled with line total: $224.38.
   Entire authorization of $200 on the GC got reversed..
   
   
4. When one of the line is getting shipped the Charge is getting opened against the Gift Card authorization which is revered in Step 4 above.

The CHARGE that is getting opened is a blind charge for a payment key of GC.
Charge sequence plays an important role in charging a payment method and authorization reversals.
In mentioned scenario, charge sequence of GC is 1 which is higher than CC and hence it will be used first instead of CC. Only when the max charge limit of the payment method is completely utilized system will move to next payment method.

When the ordeline is cancelled, system would try to reverse the CC authorization first, but since the CC is marked with do not reverse; system reverses the GC authorization.
When you have created an invoice in the system, since GC is marked with charge seq 1, system would try to use this payment method for charging. Since the invoice is already there in the system and the max charge limit of the GC is not completely used up, system will open a CHARGE against this payment method.

If there was an existing authorization in the system, the system would have used that else it would create a CHARGE without any authorization (Blind charge). This is by design.
Product does not have a configuration that would force the system to only open charges against authorizations.

Creating blind charges in this scenario is working as per design.