Are the black industry's books the same as Fantasy Flight's in content and rules?

I believe the FFG reprints incorporate the first errata. That's about the only difference between the two versions of the same books.

Both design teams seem to have had different ideas on how to work with this franchise (this is even specifically spelled out in the foreword of the Deathwatch RPG), which may explain a certain shift in rules and background design when comparing separate works of both studios, but this had zero influence on reprints of BI material, possibly for multiple reasons ranging from compatibility (apart from the errata, it'd confuse people if "the same" book had different stuff in) to simply being economic (no reason to write something that already exists).

I believe the FFG reprints incorporate the first errata. That's about the only difference between the two versions of the same books.

-Also the Calixis Sector map in the BL version contains several mistakes (planets duplicated, in the wrong location, or missing) that were corrected in the FFG version.