Hold the boot button while connecting via USB.
cd ~/katapult
make clean KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/
make menuconfig KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/
make KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/ -j4
sudo service klipper stop
make KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/ FLASH_DEVICE=2e8a:0003 flashImportant
The last line above has 2e8a:0003 where you need to replace with the flash device id for your device (which may or may not be the same). You can find it by running lsusb and look for 2e8a:0003 Raspberry Pi RP2 Boot.
See here.
Connect via CAN header...unplug USB.
cd ~/klipper
make clean KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/
make menuconfig KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/
make KCONFIG_CONFIG=.shtv3.config OUT=shtv3.out/ -j4
sudo service klipper stop
python3 ~/katapult/scripts/flashtool.py -i can0 -f ~/klipper/shtv3.out/klipper.bin -u d9543e536c0a -vImportant
Replace d9543e536c0a with your own CAN identifier.