If your 2008/09 and 2009/10 tax returns were submitted on time and they showed that you were due a tax repayment, HMRC could and probably would not repay the excess tax as you are out of time. Take a look here
for the time limits. You have four years from the end of the year of assessment to make a claim for tax overpaid through PAYE. The time limits for claiming a repayment through self-assessment are the same but HMRC can refuse to amend returns where there was an opportunity to do so within twelve months of the normal filing deadline, 31 January after the end of the relevant tax year.
Take a look at the time limits table here
. HMRC have three years from the filing date for a tax return where one has been issued to issue a determination. They have missed the deadlines for issuing determinations for 2008/09 and 2009/10 of 31 January 2013 and 31 January 2014 respectively. The have issued one for 2010/11 to protect their position and may well do so for 2011/12 if you don't get to grips with ths problem. You have until the later of three years from the tax return filing date or one year from the date of a determination to displace it by submitting your tax return.
As HMRC have missed the determination deadlines for 2008/09 and 2009/10, they will want you to submit the tax returns for those years. If you have overpaid, they will not repay the excess tax. However, if you owe tax they will want you to pay it. HMRC will continue to press for the 2008/09 and 2009/10 tax returns as they are out of time to issue determinations. If you don't, it will not reflect well on you if they open an enquiry into your taxes and may also reflect adversely on the assessment of any penalties due to a perceived lack of co-operation. It would be in your interest to submit these returns especially as it should be easy to obtain your pay and tax details (see below).
You may be able to make an arrangement to pay any determination. Over what period will be dependent on your situation and how much is owed. Every case is different.
You should be able to call the tax office on the number here
and get your PAYE pay and tax details (and P11D details) for the tax years in question from them over the phone provided that you can tell them the name of your employer(s) for any one tax year that you need the information for as well as successfully answer their security questions, NI number, address etc. Once you have those, assuming you had no other income, you should be able to complete the returns very quickly or have an accountant or tax adviser complete them for you.
The only way to overturn a determination is to complete and submit a tax return for the relevant tax year. Where you are out of time to claim overpayment relief
(the four year time limits referred to above for self-assessment), you can make a claim for overpayment relief special relief. Read from SACM12215 to SACM12270 starting here
for the criteria you need to meet to make such a claim. As you will read, a claim for overpayment relief special relief for a tax year can only be made where a determination has been issued for that tax year.
I hope this helps but let me know if you have any further questions.