react-native got build error after run pod install because project.pbxproj was updated

I was trying to upgrade react-native from 0.59.9 to 0.61.5

After run react-native upgrade, I follow the upgrade helper instruction and was able to build the project but after that, every time I ran pod install I got this error

error: my-app/ios/Pods/Pods/Target Support Files/Pods-myapp/Pods-myapp.debug.xcconfig: unable to open file (in target "myapp" in project "myapp") (in target 'myapp' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myapp/Pods-myapp.debug.xcconfig: unable to open file (in target "myapp" in project "myapp") (in target 'myapp' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myapp/Pods-myapp.debug.xcconfig: unable to open file (in target "myapp" in project "myapp") (in target 'myapp' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myappTests/Pods-myappTests.debug.xcconfig: unable to open file (in target "myappTests" in project "myapp") (in target 'myappTests' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myappTests/Pods-myappTests.debug.xcconfig: unable to open file (in target "myappTests" in project "myapp") (in target 'myappTests' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myappTests/Pods-myappTests.debug.xcconfig: unable to open file (in target "myappTests" in project "myapp") (in target 'myappTests' from project 'myapp')
error: my-app/ios/Pods/Pods/Target Support Files/Pods-myappTests/Pods-myappTests.debug.xcconfig: unable to open file (in target "myappTests" in project "myapp") (in target 'myappTests' from project 'myapp')

I can fix this by copy and paste project.pbxproj again just like what I already did before. Is there anyway I can do to not copy and paste this every time I run pod install?