CTM90670 - Corporation tax self-assessment (CTSA): Claims: Relief from double assessment
FA98/SCH18/PARA50 provides relief for double assessment. When a company has been assessed more than once for the same cause and the same accounting period, it can make a written claim for relief to the Board.
If you accept the claim the double charge is eliminated either by amendment to the assessment, or by discharge or repayment of tax.
Paragraph 50 (3) provides for an appeal against your decision on such a claim.