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Say I am in melta range and I roll 2d6 to make my Fusion Blaster's hit penetrate the hull of a Land Raider.

I have a Puretide Engram Neurochip, with which I gave my guy tank hunters.

Now I roll a 3 on the first dice and a 2 on the 2nd dice.

8 + 3 + 2 = 13

Because I got the tank hunters USR, I have to ability to "re-roll failed armor penetration rolls" (p.43 BRB).

Do I have to re-roll both dice again, as this was a failed armor penetration roll?

Or can I just re-roll one of the two dice, i.e. keep the 3 and re-roll the 2?

Your question is similar to this one, except that the melta rule asks you to add the 2d6 instead of taking the highest.

So 2d6 take highest and roll them both again if you don't like the result (but you have to keep the second pair, even if they're worse).

You reroll all the dice you rolled, unless you have a rule that allows you to roll just 1

Your penetration roll is both those dice

Now it has been a long time since I looked at the very front of the rule book but I know the answer lies there. As I am not at my Library right now I can not give you an exact page number, I apologize for that, and will have to direct you towards the index at the back to find instructions on Re-rolling. Alternative you can flick through the first few pages of the book looking for this subsection, as I am certain the information you need has been posted in the first six or so pages.

Within this section is instructions detailing how you go about re-rolling a result that uses multiple die.

Rerolls - page 5 of the main rulebook.