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If you can sell it, fine. The sales receipts become part of your turnover. Did you mean to write "can't" rather than "can"? If so, treat your sole trader business as continuing for tax purposes until you sell, scrap, or give away the stock.
You have not addressed the key question. Which company is your contract with? X Inc, or X UK Ltd? It is not the case that anyone can pick or choose which company to invoice: you must invoice the company you had the contract with.
Yes, you can sell it personally. Whatever you get for it should form part of the turnover in your final period's accounts, and the cost of the stock can be written off there too, though if you are using the cash basis that will already have happened.
Yeah, right. Obviously you just want a holiday subsidised by the taxpayer. We accountants often have clients try it on like this, in much the same way that they claim that their giant screen TV was bought as a computer monitor, or that their £2,000 bicycle was all for work journeys.
It is impossible to answer this from the facts given. There are a thousand possible reasons for this imbalance. You should appoint an accountant to deal with it.
Just from what you have said I can see several mistakes you have been making. You need to appoint an accountant and get him to review what you have done.
I recommend you ask your existing accountant (assuming you have one -if not, get one NOW) to do it for you, as he will be able to set the payroll each year at a level that is efficient both for tax and for making each year qualify towards the state pension. A payroll of one director can be done...