The FAQ says the time limit for Form 39 is not prescribed in the Income-tax Act, 2025, or in the rules. It then says it is advisable to file at least three months before you claim the relief in the return. For the employer deduction, it says the particulars may be given well before the end of the relevant tax year, so the person deducting tax can use the relief. Those are three statements. This page does not turn "advisable" or "well before" into a statutory date.
You file on the e-filing portal, online only, under a digital signature or an electronic verification code. The note's steps are: log in, open e-File, then Income Tax Forms, then File Form 39, select the relevant assessment year, fill Part A and the Part B columns that match the receipt, enter the tax figures, review column 8, submit, and file the return with the relief claimed. Part A of the form asks for the tax year, which it calls the relevant tax year as in rule 73. The steps ask for an assessment year. Both stay.
The heading above those steps still says "Process flow of filing Form 10E". The steps themselves say Form 39.
After you verify and an acknowledgement is generated, the form cannot be edited. No document is attached. Part A cannot have a blank field. The form cannot be submitted without a valid PAN. One form can cover more than one kind of receipt, in the matching section of the form.
The papers the FAQ says you may need, and then not attach, are a break-up of the receipt, a TDS certificate in Form 130, the annual information statement in Form 168, a computation for the year of receipt, and for the earlier years Form 130 or Form 16, Form 168 or Form 26AS, the returns, and the computations. It also lists proof of the lump sum, such as the employer's letter, a pension order, or a retrenchment order. The note adds the PAN to that list.
The note says a missing Form 39 can get the return marked defective, and that this holds up the filing. It does not name a section for that mark. It also says about 6 lakh Form 39 filings a year, on average, over the last five years.