It is a colloquial way to state the profit margin is being lost (eaten up) for some reason.

Bouffer is a slang verb for manger (eat)

The vous / votre redundancy is part of the colloquialism. You can find many expressions using the same pattern like:

Ça te bouffe ton forfait !

Ça vous bouffe votre capital soleil en un rien de temps.

I just found this very sentence in À chacun sa mort, by Ross Macdonald

À vous de voir. Ça vous bouffe votre marge, hein ?

The original book writes:

It’s up to you. It’s eating into your profits, isn’t it?

It means that it/something is eating into your margin/profits. Your margin is being reduced from what they could be. Or “it” could be eating away at the margin entirely. It doesn’t say explicitly if the margin is completely gone, or if there is some left.

The expression is very familiar. As noted, bouffer is the slang form of manger (to eat). The vous (and the hein at the end) are also signs of familiar language – in particular, there is no real reason for that vous to be there from a grammatical point of view. The sentence could also be:

Ça bouffe votre marge, hein?

or:

Ça vous bouffe la marge, hein?

(thanks Papa Poule)