In my case the issue was caused by a local android only plugin. I created a dummy podsec file for the plugin, then ran:
cd ios
flutter pub get
pod install
pod update
It seems like I need to do these steps after every xcode project clean now.
$ flutter doctor
Doctor summary (to see all details, run flutter doctor -v):
[✓] Flutter (Channel stable, v1.17.4, on Mac OS X 10.15.6 19G73, locale en-AU)
[✓] Android toolchain - develop for Android devices (Android SDK version 30.0.0)
[✓] Xcode - develop for iOS and macOS (Xcode 11.6)
[✓] Android Studio (version 4.0)