I'm upgrading a React Native project to v0.63.4, and am getting a similar error to the one in this question. In the accepted answer to that question, the user shares what the contents of your Podfile should be. That's the same as what the React Native upgrade helper indicates the Podfile should be.
The Podfile in my project contains a bunch of lines like
pod 'FBLazyVector', :path => "../node_modules/react-native/Libraries/FBLazyVector"
pod 'FBReactNativeSpec', :path => "../node_modules/react-native/Libraries/FBReactNativeSpec"
pod 'RCTRequired', :path => "../node_modules/react-native/Libraries/RCTRequired"
What I Want To Know: Should I remove all lines like that ^ and make the Podfile identical to the one in the React Native upgrade helper? Or should I still include those lines somehow?
Follow the instructions from the upgrade helper. Your Podfile will likely be very minimal once you're done).
Podfile.lock and the Pods directory can be safely deleted (and probably should for something like this, since it's a big change) -- they'll be regenerated on pod install.