In the case of individuals, filing tax returns is mandatory only if there is taxable income or if the conditions realting to payments towards credit cards etc are applicable . Non filing of returns is, in my opinion, not an isssue for claiming rebate u/s 89(1).
If the arrears include the years for which you declared pension income, then take the same amount as received during those years for the purpose of computation of rebate u/s 89(1) and make suitable adjustments in the subsequent years. Then work out the rebate u/s 89(1). Now work out the rebate by taking correct amount. Claim the rebate which is less under both these scenarios. This is to err in favour of revenue as there may not be signifcant difference in claiming the rebate claimable and claimed.
Please submit 10E to the Pension office to consider the rebate while deducting tax on pension amount. If its not considered by the Pension Office for any reason, you may file it on or before filing your IT Return by the due date.
10E will be considered while processing the return by the CPC.