If you are self employed(Limited Company) and pay into your pension through the company then you have nothing to subtract from your HMRC earnings, because this is not declared for income purposes. ie income to company is 60K, you pay yourself 50K and company pays 10K into your pension. HMRC sees £50K earnings with no deductions for pension.
If you are PAYE and earn 60K and pay 10K pension into personal pension they will see the total gross(60K) and then take into account the 10K pension as a deduction from the assessment.
I may have missed the point of your question though and not sure it it matters whether company provided or personal pension, other than above points.
And finally, I had exactly the same situation as you. Annual assessment time, I wrote to them and told them I had earned more. They ignored and based it on what HMRC had on file - as it was April the new figures were not available to HMRC. So my ex appealed on grounds of income diversion, took me to tribunal but then the tribunal was cancelled because by the time CMS looked to confirm if I should go to tribunal, HMRC had caught up and could show the higher earnings I had already told them about! So they reassessed and cancelled the tribunal and wrote a letter to me saying I had been a naughty boy for withholding higher earnings :-)
lol CMS can be real jokers. when i registered, they sent a letter to my ex writing that they checked my tax records and my income is 0 so i dont have to pay anything:p so i rang them and told them my income figure last year was 0, but i have a dividend figure and that was my income for that year.
had i stuck with their stupid decision i could have easily ended up in a tribunal.