No matter the situation, If you own a perticular skin, say Brick, you cannot upgrade you base to that skin.
It will tell you its already upgraded but no changes will happen. I have had this issue brought to me from other users for shipping container as well.
They couldn't upgrade their base to shipping container from the default becuase they own shipping container, but as soon as I went on their TC I could upgrade everything with no issues as I don't own shipping container.
Could this error please be addressed.