The Central Board of Direct Taxes (CBDT) has issued a circular in this regard where if the taxpayer has tax refund pending or wish to carry forward his losses and missed the deadline of filing of tax returns, then he can file an application to the Income tax commissioner or the prescribed authority.
These are the parameters based on which applications can be accepted or rejected by the income tax department:
a) The claim is correct and genuine
b) Case is based on genuine hardship on merits
c) Income is not assessable in the hands of any other person under the Income Tax Act
d) The refund has arisen as result of excess tax deducted or tax collected at source, advance tax or self-assessment tax.
If you have not paid taxes for FYs 2015-16 and 2016-17, then it is advisable that one should at least pay all your taxes and interest along with it as applicable under section 234A, 234B or 234C, even if they cannot file the ITR post March 31, 2018.
If the taxes you are supposed to pay have been cleared but if you have not filed your ITR before March 31, 2018, then you do not have the option to file their ITR now or to apply for condonation of delay. However, the department can issue a notice under section 271F for levying of penalty on non-filing of ITR. The maximum penalty in such a case is Rs 5,000. No penalty will be levied if there is a genuine reason for such non-compliance and if the income tax officer is satisfied with the reasons.