As per the information provided by you it appears that you can see the issue under the compliance module and the return is time barred.
If this is the case, then the best option is to pay the respective taxes with interest and keep it for your record, whereas in the module you can select Return under process/ Others. You can also mention that the respective taxes with interest has been paid in order to avoid future complications.
Trust this clarifies your query.
Feel free to call back/ get back in case of further clarifications.
Rohit R Sharma
BCOM, ACA, LLB - GEN, CERT. FAFP