Why was my Section 89 relief on salary arrears disallowed?

Why the relief disappears even when your numbers are right

Section 89 gives relief on salary arrears or advance salary so it isn't taxed harder just because it landed in one year instead of being spread across the years it was actually earned. The relief itself is calculated correctly by most people. What breaks it is a process step: Form 10E has to exist, for the right assessment year, before the ITR is filed, or the department's automated processing disallows the relief entirely and tells you about it afterward, through an intimation under Section 143(1), not before.

What people get wrong about this

Filing Form 10E after the ITR, thinking it will still be picked up, is the single most common mistake. It won't be, the ITR is processed against whatever existed at the time, and a late Form 10E needs its own rectification request to actually take effect.

Assuming a revised return fixes this is the second. A revised return doesn't retroactively attach a Form 10E that wasn't there when the original was processed, a Section 154 rectification is the actual mechanism here.