I don't use the Blackout Pack, only the black contacts. And it works fine. I use the pack from here: http://forum.xda-developers.com/showthread.php?t=2261854 for CM-Icons on SMSI figured it out already, you have to flash the Blackout Pack first and after that the black contacts. Otherwise you loose the Apps. It doesn't even work, when i add the black contacts into the Pack, only when i flash them separately. It's original an XT910 apk, so it was more an experiment
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Only thing i lost, like HSD said before, is the AOSP-Dialer. Its something i can live with, I don't use the dialer very often. Mostly i make calls from the contacts.apk