Xcode corrupts project.pbxproj everytime I try to

Question

Currently on react-native 0.58.3 and react 16.6.3.

The project builds and runs correctly when using react-native run-ios

However if I try to build using Xcode directly (to test on device for example), it will fail and corrupt the project.pbxproj file with extra entries that make builds fail with react-native run-ios as well.

Below are copies of the project.pbxproj before and after Xcode mangles it:

Before, working:https://pastebin.com/g5fUL1zn

After, not working:https://pastebin.com/M76vinaV

XCode Build Error Log:https://pastebin.com/8TsDD9HS

The main error I am getting is:

error: /Users/bh/Documents/DashiftReactNative/node_modules/react-native/ReactCommon/privatedata/PrivateDataBase.h: No such file or directory

Xcode does mess around with the PrivateDataBase entry...