Also binkpack works for many .bk2 videos too. I always check it before compressing the whole game. If they are incompatible i usually use Video Rad Tools to compress them to bink1 (output will be higher if you dont touch the ratio). I use a ratio output of around 80%, there is a little bit of quality loss, not much really but size is also a bit smaller and after that you can rename the files to .bk2 and use binkpack on that.
Edit: Oh, and on some games there is only 1-2 videos incompatible with binkpack, for example on AC Unity it fails only on one .bk2 file and on Black Flag on half of the bink files. On latest codemaster games all videos are non working, at least from my tests.