Advice remains to be check the facts. These letters are not a demand or an assessment. You should check to make sure that HMRC's revised record of your employment is actually correct. Next check your tax codes to see if the figures actually reflect your circumstances. If anything appears wrong contact your tax office.
Unless the underpayment is more than £2,000 the recovery process will by through limiting your tax code for the 2011/12 tax year (commencing 6 April 2011).
There may also be circumstances where any arrears can be written off. This extra statutory concession can apply where HMRC have been supplied with all of the relevant information within 12 months of the end of the tax year and they have simply failed to use it.
If you want to challenge your new calculation you should contact HMRC on the phone number provided and request they do so.