Translation:Your boots are not in the wardrobe, but under the table.
Your boots are not in the wardrobe, but under the table, is not accepted.
You are right and this is ambiguous. Boots are grammatically singular whether it is one boot or a pair and I think the verb has to agree.
I came here to discuss this comment and now I can't go back to where I was. This happens often so I don't go to discussion much. So annoying to have to start again from the beginning of the lesson!