You perform upkeep on your ships to keep them operating to your requirements, which includes fuel and repairs, ammunition and limpets, materials for synthesis, and of course any NPC crew members.
These upkeep items entail a credit cost, which your use of the game loops (often referred to as playing) has to cover. It seems the most likely reason for upkeep on a carrier would be for maintaining crew. While you have the same type pf upkeep on a multi-crew ship albeit it almost certainly on a smaller scale, on a Fleet Carrier, no crew would mean no functioning services, but it may also mean no maintenance and repairs, which would result in a derelict craft. That could be why it gets decommissioned.
Again, more detail is needed about why, how much, and how long, but as a concept it is sensible, and fairly comparable with existing upkeep in the game, if the scaling is made proportionate.