It cannot be filed through online mode but can be done through offline mode by filing application under section 119(2)(b) . It totally depends on the concerned commissioner to whether approve or reject the application.
in income tax site there is option in filling " Are you filling u/s 119(2)(b)/92CD and option for this is Yes/No. then can I file return under this option?
if you have any refund amount to be claimed and due to reasons beyond your hands, you were unable to file ROI within due time, then after filing ROI, you have to file condonation of delay application before jurisdictional CIT, mentioning the reasons due to which you were prevented from filing ROI. if CIT condones delay, your ROI will be processed and refund will be issued.