Just tested the changes to make a config for the PRO board. Change your boards.txt file to:
menu.cpu=Processor
flutter.name=Flutter Pre-production hardware
flutter.vid.0=0x2341
flutter.pid.0=0x003e
flutter.upload.tool=bossac
flutter.upload.protocol=sam-ba
flutter.upload.maximum_size=65536
flutter.upload.use_1200bps_touch=false
flutter.upload.wait_for_upload_port=false
flutter.upload.native_usb=true
flutter.build.mcu=cortex-m3
flutter.build.f_cpu=64000000L
flutter.build.usb_product="Flutter Pre-release"
flutter.build.board=FLUTTER
flutter.build.core=arduino
flutter.build.extra_flags=-D__SAM3S1A__ -mthumb {build.usb_flags}
flutter.build.ldscript=linker_scripts/gcc/flash.ld
flutter.build.variant=flutter
flutter.build.variant_system_lib=libsam_sam3s1a_gcc_rel.a
flutter.build.vid=0x2341
flutter.build.pid=0x003e
flutter_r2.name=Flutter Basic
flutter_r2.vid.0=0x2341
flutter_r2.pid.0=0x003e
flutter_r2.serial.0=0x5
flutter_r2.upload.tool=bossac
flutter_r2.upload.protocol=sam-ba
flutter_r2.upload.maximum_size=65536
flutter_r2.upload.use_1200bps_touch=false
flutter_r2.upload.wait_for_upload_port=true
flutter_r2.upload.native_usb=true
flutter_r2.build.mcu=cortex-m3
flutter_r2.build.f_cpu=64000000L
flutter_r2.build.usb_product="Flutter Basic"
flutter_r2.build.board=FLUTTER_R2
flutter_r2.build.core=arduino
flutter_r2.build.extra_flags=-D__SAM3S1A__ -mthumb {build.usb_flags}
flutter_r2.build.ldscript=linker_scripts/gcc/flash.ld
flutter_r2.build.variant=flutter_r2
flutter_r2.build.variant_system_lib=libsam_sam3s1a_gcc_rel.a
flutter_r2.build.vid=0x2341
flutter_r2.build.pid=0x003d
flutterPro_r2.name=Flutter Pro
flutterPro_r2.vid.0=0x2341
flutterPro_r2.pid.0=0x003e
flutterPro_r2.serial.0=0x5
flutterPro_r2.upload.tool=bossac
flutterPro_r2.upload.protocol=sam-ba
flutterPro_r2.upload.maximum_size=131072
flutterPro_r2.upload.use_1200bps_touch=false
flutterPro_r2.upload.wait_for_upload_port=true
flutterPro_r2.upload.native_usb=true
flutterPro_r2.build.mcu=cortex-m3
flutterPro_r2.build.f_cpu=64000000L
flutterPro_r2.build.usb_product="Flutter Pro"
flutterPro_r2.build.board=FLUTTER_R2
flutterPro_r2.build.core=arduino
flutterPro_r2.build.extra_flags=-D__SAM3S1A__ -mthumb {build.usb_flags}
flutterPro_r2.build.ldscript=linker_scripts/gcc/flash.ld
flutterPro_r2.build.variant=flutter_r2
flutterPro_r2.build.variant_system_lib=libsam_sam3s1a_gcc_rel.a
flutterPro_r2.build.vid=0x2341
flutterPro_r2.build.pid=0x003d