One of my players lost the armour on his arm, and decided to replace it with a single carpace plate (I've allowed that). The thing is that previously he had the full flak armour, AP 4 on all locations, but now he has a 5 on one arm. Should I still treat the rest of his body as having an AP 4 or get back to individual armour values? I haven't found anything about this issue in rulebook or errata. What are your opinions on this matter?

Only the best armor counts in a location. So if he has flak all over and carapace on one arm, the one arm just have more armor then the rest of him.

You misunderstood me. He had flak armour on all locations but lost his arm. Now he bought a carpace for his arm, while still retaining the flak armour on all other locations. However the single falk armour parts only give you 3 AP with full flak giving 4. I wanted to know if the carpace on his one arm should give him 4 AP on all other loactaions (and 5 AP on that one arm), or since it's not flak, all other locations should have AP of 3?

The rest of his armor should still be ok, so keep it at 4?