Have to "Replace" iOS project every build because of Linker Errors

Ever since I added Chartboost and Applovin into my project, I have to replace the iOS project instead of appending. I get a bunch (over 100) of Linker Errors if I append. It took me over a day of frustration removing and reimporting the Chartboost and Applovin SDKs and tweaking the build settings before I figured out that replacing the Xcode project would fix the errors.

I'm asking this question because it's very inconvenient because due to another Unity bug, I have to tweak the app delegate in order to receive push notifications on iOS 8 every time I rebuild. Has anyone else experienced this and did you find a fix?