Lip Reading is a skill in Dark Heresy, but it's not covered in the Rogue Trader rules. However it still appears on the Rogue Trader character sheet.

So is it a skill which can be used in Rogue Trader or not? And if not, what do we use instead?

I'm guessing that they decided to cut the skill due to its extremely limited use but forgot to take it off the character sheet.

For lip reading now I'd either go with a straight Perception check, since that's what Lip Reading is based off in DH. Perhaps replace it with an Awareness test?