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You already have a phone app so if it isn't there, how can you lose the one you already have? The phone app is part of your rom. (I flash gApps, then these.)![]()
Wait so you flash another set of gapps before the inverted ones?

That's what I do....
Create recovery backup.
Flash rom, gApps recommended by that rom, custom kernel (GlaDOS).
Reboot, if running ok, I continue:
Flash inverted apps, and inverted email (not usually included with apps)
If there's an issue with something, I'll restore my backup.
I assume that there's stuff in Google's apps that aren't included in the inverted apps so I flash both.![]()


bump...
Aroma (interactive - pick apps you want installed) and Quick Flash both working great here with Codename Android on two different devices. QF version had drop box, which I didn't see in Aroma. Just flash from CWM or TWRP.
As always, have a recovery backup before flashing.
http://forum.xda-developers.com/showthread.php?t=1797292