I apologies for my terrible English, ill try explain it more clearly.
Just before I explain the situation, in the scenario, pretend everything I do will already have admin access.
Anyway on to the point, I am not sure if you would get the same thing, but on my base if I did /shop remove (lets say water)
-The base jettison the cargo as intended
-But prevents you to restock the same item temporarily (about 30 minutes+)
Now lets say if I got my 1000 cargo transport and carried about 500 H fuel and 500 Water, which I brought to resupply the base with. After shop remove command, when I go to the commodity trader, the water I have in my ship's cargo hold doesn't show up at all. The H-fuel however will still appear on the ship as normal and be able to sell it.
The base will still show the cargo hold meter on your transport as still there, and the water will still be in the ship when you undock from the station, but the water simply wont show up while you are trading inside the station. This effect last a while before return to normal again
Not sure if its a bug or intended, but you can try and see if its the same for you ... and sorry if the amount of "water" i type made you abit peckish for a drink.
