Query regarding refund claiming for relief under sec 89

I have got salary Arrears from FY 2005-06 to FY 2014-15. I have submit 10E, annexure 1, a Table ( showing Total income of the relevant previous year, Salary received in arrears relevant previous year , tax on total income before & after adding arrears and the differences in tax), a separate sheet showing the split arrears and calculation the tax amount. But my employer does not ready to give from 16 with considering the relief under section 89. My query is : if my employer give me from 16 showing the total income including the arrears and deduct the tax accordingly, can I get refund after filling the income tax return including 10E and annexure I in income tax website?