Omega reputation ground gear accolades do not count items that have been slotted for upgrade.

hawkrunner

The accolades (and therefore associated costumes) for Omega reputation ground gear sets (i.e. MACO, Omega Force, Adapted MACO) do not seem to recognize items that have been slotted for upgrade, and if the item was once checked off, slotting it for upgrade will cause it to un-check itself. I've been holding out on spending the marks and dilithium to re-acquire these items through the reputation in the hopes that this bug will be fixed.

These items also cannot be re-claimed from the DS9 Vendor once they have been slotted for upgrade.